Georginio Rutter should have doubled their advantage after the break when he forced a save from Lions keeper Matija Sarkic, before his rebound was deflected on to the post.
Second-half substitute Dan James wrapped up the win with a close-range finish as he worked on to Rutter’s fantastic ball across the face of goal with 11 minutes remaining.
The result lifted Leeds above Leicester on goal difference, having played a game more than the Foxes, while Ipswich are a point behind in third place.
Enzo Maresca’s side were not in league action this weekend, losing 4-2 at Chelsea in the FA Cup quarter-finals.
Millwall remain in 16th and four points clear of relegation, having seen a four-game unbeaten start under returning boss Neil Harris come to an end.
Leeds dominated the first half and were rewarded for their pressure when Italy forward Gnonto received the ball in the 33rd minute and took a turn before firing home left-footed from distance past Sarkic.
Sarkic kept the visitors within reach when he pulled off a fabulous diving save to deny Crysencio Summerville, but Leeds arguably should have been awarded a penalty soon after.
Already on a booking, Jake Cooper went in high with his knee and appeared to catch Joe Rodon in his face, however referee Stephen Martin did not point to the spot.
Daniel Farke’s side largely dominated proceedings as the Lions had Sarkic to thank for keeping them in contention.
Rutter’s quick-fire pair of chances on goal, during which he was denied by Sarkic, was the closest Leeds came to padding out their advantage.
Michael Obafemi did weave his way into the Leeds box as the visitors made a rare foray forward late on, but his solo effort finished with him firing high and wide while under pressure from Ethan Ampadu.
Patrick Bamford also went close at the other end, and would have finished coolly were it not for some impressive defending from Japhet Tanganga.
But James showed composure to confirm the home side’s 12th win in the last 13 games.
