Goals either side of the break secured progression to Roberto Martinez's side's first ever FA Cup final despite a spirited second-half display from Kenny Jackett's Lions
Shaun Maloney gave the Latics a deserved lead mid-way through the first half after sliding in to convert a curling cross from Arouna Kone.
And despite a spirited second-half showing from their Championship opponents, Callum McManaman doubled Wigan's lead to seal the result after 78 minutes.
Wigan boss Roberto Martinez recalled Ali Al-Habsi for the first time since the beginning of March but kept an otherwise unchanged line-up from the Latics' 1-1 draw at QPR last Sunday.
Millwall, meanwhile, made three changes from the Lions’ 2-1 loss to Sheffield Wednesday on Tuesday as Jack Smith and James Henry returned to the side, while the experienced Rob Hulse was overlooked in favour of Andy Keogh.
And it was Keogh who got the ball rolling inside the first minute, rising above Antolin Alcaraz to direct a glancing header at Al-Habsi’s goal.
McManaman was next to come close as the Wigan forward stung the palms of David Forde from range.
But there was nothing Forde could do to stop Maloney 20 minutes later as the Scotland international reacted superbly to a pinpoint cross from Kone to edge his side into the lead.
The Ivorian was sensational in the build-up, picking the ball up inside the Millwall half and surging forward to pick his teammate out with supreme precision. Maloney was on the stretch inside the danger area but produced a fine finish to give Wigan the lead they deserved.
Minutes later, Scharner drew the Millwall keeper into action once again and the signs were worrying for the Championship side.
The Lions kept things tight until the break, however, despite Jordi Gomez coming close late in the half and Wigan enjoying a remarkable 72% of possession in spells.
More was needed from Kenny Jackett's side as a squad bereft of form looked overwhelmed by the occasion and offered very little going forward.
But no immediate improvement came forth and, instead, Wigan continued to press. McManaman threatened once more on the 50-minute mark, cutting in from the left and curling an effort just past the far-post.
Millwall enjoyed their best chance on 58 minutes, though, as Chris Taylor burst forward only to be brought down just outside the Wigan danger area. James – usually a reliable set-piece taker – stepped up to the ball and curled the ensuing free kick just over the bar.
Then, Alan Dunne sent a dangerous low cross into the area and Keogh was denied by a last-ditch tackle. The Lions were starting to roar.
But on 78 minutes, Wigan made sure of the tie – and who else but McManaman to do it. Kone started the move off once again but it was Gomez who slid an incisive pass through to the 21-year-old, who rounded the keeper to finish off in style.
Martinez’s men had completed the job – and a day of destiny now awaits them in the final - but in-fighting amongst the Millwall fans soured the otherwise good natured contest.