David Prutton was sent off in the 66th minute and Mark Yeates struck the winner from the resultant free-kick.
Leeds lacked their captain Frazer Richardson with a dead leg, while a hamstring injury kept former Leeds defender Matt Heath out of Colchester's side. Alan Maybury, another ex-Leeds defender, who joined the visitors as a free agent on Thursday, made his debut.
McAllister wanted his team to toughen up and referee Nigel Miller had words with Robert Snodgrass and Colchester's Welsh striker Jermaine Easter for an off-the-ball confrontation.
Easter was then injured in fouling Fabain Delph and had to be replaced in the 26th minute by Scott Vernon who was celebrating his 25th birthday.
Yeates' tricky runs down the left worried Leeds' defence but Colchester fell behind in the 35th minute.
Goalkeeper David Lucas aimed a long kick upfield for Snodgrass, who sprinted clear of Chris Coyne before neatly stepping inside Paul Reid and stroking the ball wide of keeper Jimmy Walker for his fourth goal of the season.
Snodgrass could have had a first-half hat-trick but his close-in header from Delph's cross was straight at Walker and he also shot into the keeper's body when in the clear.
Colchester's 45th minute equaliser was controversial as the referee allowed Yeates to take a corner while defender Rui Marques was off the field changing his shirt.
Dean Hammond reached the ball ahead of three Leeds defenders to head a soft equaliser - the latest in a series of recent goals McAllister's men have conceded from set-pieces.
Former Middlesbrough and Derby striker Malcolm Christie made his league debut for Leeds when he replaced the ineffective Neil Kilkenny just after the hour.
Prutton was sent off for his second bookable offence when he fouled David Perkins in the 66th minute and Yeates scored direct from the free-kick, curling the ball in from the left.
Hammond cleared a header from Snodgrass off the line as Leeds tried and failed to find an equaliser.