Southend did enjoy sustained periods of possession early on but struggled to create clear cut chances and never looked like scoring.
Leeds eventually hit back and, in the 20th minute, they almost broke the deadlock when Robert Snodgrass' header from Gradel's right-wing cross was impressively tipped over by Blues goalkeeper Steve Mildenhall.
The Shrimpers shot stopper then easily gathered an attempted chip from Snodgrass before Jermaine Beckford, who received tremendous amounts of stick from the home supporters, headed Neil Kilkenny's driven cross wide of the left post.
Moments later, Beckford fired a deflected left-foot shot wide of the opposite upright, but having survived those scares, Southend replied with the recalled Matt Paterson sending an ambitious 25-yard shot over the crossbar.
In reply, Leeds skipper Richard Naylor headed a Kilkenny corner off target when he should have done better, but attention then again turned towards the stands as the Yorkshire side's fans continued to slate Beckford, who has netted 27 goals this term.
Chants of "You're not fit to wear the shirt" echoed around the ground as Leeds fans apparently feel his recent performances have lacked heart and show he will be leaving at the end of the season.
Those frustrated supporters could have been feeling much worse on the stroke of half-time as Scott Vernon broke into the box.
But the striker, who had Stuart O'Keefe completely free to his left hand side, lost his footing before sending a weak effort into the gloves of home goalkeeper Shane Higgs.
That was to prove to be Southend's only opportunity in front of goal and Leeds made the most of the let off, but only after a double substitution in the 58th minute.
That saw the barracked Beckford replaced by Becchio in attack, while Bradley Johnson also entered the action.
And the changes did the trick as, just two minutes after their arrivals, Simon Grayson's team broke the deadlock with a move which began on the edge of their own penalty area after O'Keefe had lost possession.
The ball quickly moved upfield before Gradel cut in off the left hand side and unleashed a low left-footed shot from 14 yards which took a wicked deflection of Pat Baldwin before nestling into the bottom right hand corner of the net.
Blues replied with a substitution of their own as Francis Laurent replaced Paterson in attack, but Leeds remained on top.
They soon almost made it 2-0, but Mildenhall did well to keep out a close range header from Snodgrass.
A slice of luck followed that chance as Leeds should have been reduced to 10 men in the 78th minute following a shocking challenge from Johnson on Jean-Francois Christophe.
Referee Eddie Ilderton seemed certain to send off the substitute and even had the red card in his hand before seemingly changing his mind and just booking the midfielder.
Southend responded with a stretching Laurent heading a Francis free-kick off target, but with 83 minutes on the clock, Leeds doubled their lead to make certain of all three points.
Gradel was the provider this time as his accurate left-wing cross just evaded Adam Barrett and perfectly picked out the head of the popular Becchio, who made no mistake with an assured header from six yards.
Jonathan Howson should then have made it 3-0 but he could only send his low 12-yard shot straight at Mildenhall.
Southend's final throw of the dice came in the 86th minute when Jean Yves M'Voto, who is normally a defender, came on as a makeshift striker.
He headed a right-wing cross from Francis wide late on, leaving the Shrimpers and their loyal fans to make another long journey home empty-handed.