Colchester were baffled by referee David Phillips' decision to award a free-kick, which was taken by Robert Snodgrass for Bradley Johnson to head into the bottom right corner.
Colchester reacted superbly to the set-back and deservedly equalised in the 57th minute when a superb piece of Kevin Lisbie skill won a penalty which he then emphatically converted.
Rui Marques gave away his second penalty of the season with a foul on Lisbie, who blasted the spot-kick into the top corner.But with the home side looking like they might push on for a winner, Leeds were again gifted the lead when Alan Maybury's tame header was poked home by the in-form Beckford after 63 minutes.
It was the former Wealdstone hit-man's fifth goal in as many league games and saw Leeds equal a club record that has stood since 1973 by securing their seventh successive win from the season's start.
Caretaker boss Joe Dunne, in what is likely to be his final league match in charge of the U's, kept faith with the forward line of Scott Vernon and Lisbie even though Clive Platt was available again following a three game suspension.
Former Leeds player Maybury came into the team to make his first league start of the season, replacing fellow right-back Lee Beevers after he dislocated his shoulder against MK Dons last Saturday, while want-away midfielder David Perkins was once again left on the bench after he handed in a transfer request last week.
Leeds kept the same side which took Tranmere Rovers apart last Saturday at Elland Road with Mike Grella back on the bench after his start against Watford in mid-week.
The league's top goalscorer Beckford showed early on his danger when he nipped away from Magnus Okuonghae just inside the U's half. The big centre-half took him down and was lucky to escape without a booking.
Minutes later Beckford had the ball in the net from Jonathan Howson's pass, but was clearly offside and was rightly flagged after the home backline perfectly timed their step up.
Colchester's first effort of the match came after eight minutes when David Fox let fly from long range and Leeds keeper Shane Higgs clawed the ball around the post in front of the vociferous travelling support.
Leeds were on top in the opening exchanges and Beckford once again had a goal marginally ruled out for offside in the 15th minute following a smart first time ball around the corner from Argentine strike partner Luciano Becchio.
This time there was just inches in it and Beckford, having wheeled away in celebration after his cool finish, was disgusted with the linesman's decision.
Beckford almost created something out of nothing after 23 minutes. A long ball over the top was initially won by the towering Okuonghae but Beckford, at the tightest of angles, hit the dropping ball with venom and keeper Ben Williams was forced to stop the ball finding its way into the bottom right-hand corner.
For a split second Colchester thought they had a penalty on the half hour mark when, amongst a crowd of players down the left hand side, Vernon chipped the ball up onto Michael Doyle's arm. The referee ruled that the incident was just outside the box though and Fox wasted the resulting free-kick.
The game always had a niggly feel to it and it was something of a surprise that it took until the 39th minute for a card to be produced.
Then three followed in the space of a minute. First Maybury tripped Johnson, the Leeds man pushed him in retaliation and the pair were booked. From the ensuing free-kick Beckford inexplicably pushed Baldwin in the box and he too saw yellow.
Then it was Colchester who got more into the game as half-time approached. A quick free-kick from Marc Tierney led to a corner and Ashley Vincent eventually blazed over after Leeds struggled to clear.
Izzet was fortunate not to be added to the referee's book right on half-time when he fouled Johnson on his way to goal. Snodgrass fired just over from the 25-yard free-kick.
Leeds opened the scoring within seconds of the second half. Okuonghae and Snodgrass came together on the byline, the referee awarded the free-kick in the away side's favour and it was all too easy for Johnson to beat Baldwin to the ball and head home Snodgrass's delivery.
Colchester immediately came the closest they had to scoring all match when, two minutes later, Simon Hackney's superb free-kick from just outside the box was turned over by Higgs when heading for the top left corner.
The U's had reacted superbly to their set back and equalised in the 57th minute thanks to a moment of magic from Lisbie.
In one smooth movement the on-loan Ipswich striker brought the ball down from high in the box and turned inside Rui Marques. The centre-half took him down and a penalty was awarded. Lisbie then stepped up and smashed a brilliant spot-kick into the top right corner for his fourth of the season.
Now on top, Colchester were fired up as they chased a second, however,
they received two yellow cards in the space of three minutes after the leveller.
First Izzet was booked for a foul before Vincent followed him for remonstrating with the linesman in a separate incident.
All Colchester's hard work was undone in the 63rd minute though with a piece of terrible defending. A routine ball into the box was headed tamely by a diving Maybury, allowing on-the-spot Beckford to poke home from six yards in front of his delighted fans. It was his fifth league goal in as many games.
Platt, then Perkins, were introduced as Colchester chased the game, but Leeds' defence, led by the excellent Patrick Kisnorbo, continued to hold firm.
At the other end Leeds continued to prove a threat and Becchio came close with a low shot from outside the area following a fine Johnson back heel flick.
Colchester pushed hard for an equaliser in the four minutes of stoppage time but there was no way through as they fell to their second successive 2-1 defeat in the league.
Colchester United: Williams, Maybury, Okuonghae, Baldwin, Tierney, Vincent (Perkins 74), Izzet, Hackney, Fox (Wordsworth 83), Lisbie, Vernon (Platt 67).
Subs Unused: Cousins, Thomas, Holt, Lockwood.
Thanks to Stuart Watson of Green'Un 24 for the match report
The Green Un
The Green Un
YEP chief football writer Phil Hay rates how United's players performed at Colchester;
Shane Higgs: Made to work a couple of times from long range, but proved equal to the best that Fox and Hackney could offer. Lisbie's penalty was unstoppable...7/10
Jason Crowe: Whilst making few major errors, Crowe did not seem completely comfortable and Colchester were happy to launch most of their attacks down the left wing...6/10
Rui Marques: Lisbie tied him in knots to win the penalty and Marques' tackle was misjudged. But in the main he made the right decisions in the key areas of the game...7/10
Patrick Kisnorbo: Rock solid yet again and Kisnorbo's absence next weekend is a huge loss. Read the game perfectly and may have won the match with his late block...8/10
Andrew Hughes: Steady with his distribution and ensured that Colchester's threat was almost non-existent on his side of the field...7/10
Robert Snodgrass: Cut a frustrated figure with his body language in the first half but he delivered a perfect free-kick that Johnson could not fail to feast on...6/10
Jonathan Howson: Izzet tried to glue himself to Howson, whose attacking influence ebbed and flowed, but his effort in the dying moments when Leeds were under heavy pressure did him credit...7/10
Michael Doyle: United needed a player like Doyle on Saturday - someone who was willing to fight fire with fire in midfield. Not at his best but stood up for the players around him...6/10
Bradley Johnson: Johnson's goal - his third of the season - on Saturday was a gift but he is making a consistent impact this season. Would have liked to have seen more of the ball though...7/10
Luciano Becchio: A display which might have gone unnoticed but was absolutely selfless. Becchio showed the strength of a bull and the occasional delicate touch in a very physical clash...8/10
Jermaine Beckford: Denied what would have been a good goal by an errant offside flag, but you cannot keep Beckford down. A sniff of a chance was all he needed...7/10
Substitutes; David Prutton (for Snodgrass, 80)...5/10
Lubomir Michalik (for Marques, 87)...5/10
Enoch Showunmi (for Becchio, 90)...5/10
Subs Unused: Neil Kilkenny, Andy Robinson, Mike Grella, Casper Ankergren