A fortuitous scramble on 15 minutes and whipped free kick later in the second half from Ross McCormack were enough for Leeds United to clinch victory at Elland Road in Latics' first game without former manager Owen Coyle.
Graham Barrow took charge a side which dominated in possession on the evening, but couldn't find their way past Paddy Kenny in the host's goal.
Stepping in to lead Latics on the night, Barrow brought in Scott Carson, James Perch, Chris McCann and Jean Beausejour, which gave a new shape to the team with three at the back.
Leeds' direct style of play caused Latics problems on the night, with both goals coming from set pieces, and the home side showed their intent from the early stages as they aimed to link up between strapping centre forward Matt Smith and the in-form Ross McCormack.
After a period of initial pressure, Leeds took a somewhat fortunate lead on 15 minutes when a corner was headed back across goal by Tom Lees and into the path of McCormack who forced the ball over the line despite the best efforts of Ben Watson to clear off the line.
A similar pattern of Leeds' play followed, but towards the break it was Latics who came into their own.
Will Keane, receiving his second consecutive start, latched on to two chances with just Leeds' keeper Kenny to beat, but first the stopper saved with his face from close quarters and Keane's second chance following a defensive error was pushed away as he struck the ball straight at Kenny.
As the half time neared Emmerson Boyce came agonisingly close when he headed a Beausejour corner into the ground and narrowly over the cross bar.
The start of the second 45 continued in the same manner, as Latics built up possession and pinned Leeds into their own defensive third.
Latics attempted to create gaps in the Leeds' rearguard, but the hosts held firm, denying genuine chances to be created.
After the pressure died down, a mistake from Ivan Ramis almost allowed Smith to double Leeds' lead, but in a three-on-one situation Scott Carson made himself big to deny the former Oldham Athletic front man.
Leeds did eventually score a second goal to push the tie away from Latics, when a whipped, in-swinging free kick from McCormack crept all the way in past Scott Carson.
A late push wasn't enough for Latics, with substitute McManaman fizzing an effort from the edge of the area over the cross bar, before having an opportunity at the near post stolen off his toe when it looked likely that he would convert.
Leeds grabbed the three points, but Latics' possessional dominance was an encouraging sign, and as Graham Barrow said in his post match interview, "we just need to find that formula of movement in the final third."