In a game that saw three players red carded, midfielder Abdou headed the vital opener with 16 minutes remaining before sub Magaye Gueye made the points safe with a clinical 92nd-minute strike.
With the stakes high in a game that pitched third from bottom Wigan with a Lions outfit sitting just one place below, a nervy first-half was very much a cat and mouse affair as neither team really stamped their authority on proceedings.
The visitors nearly stole the lead early on when James McClean's third-minute shot seemed to clip the outside of the post before Millwall eventually cleared the danger.
Aiden O'Brien did superbly to win possession on 18 minutes, but Latics keeper Scott Carson raced out of his goal and averted the danger quickly.
The best chances of the opening half fell to Wigan striker Marc-Antoine Fortune, who saw David Forde expertly tip his goal-bound header from Gaetan Bong's cross over the bar, whilst at the other end O'Brien's 40th-minute header was on target, but lacked power and was comfortably dealt with by Carson.
The game sprung to life after the break, and O'Brien forced Carson into a splendid save with a curling left-foot effort that the keeper pushed away at full stretch to deny Millwall after 50 minutes.
Young defender Sid Nelson got the home crowd on their feet and really brought them into play with a brave, diving header to win possession on the halfway line.
The home fans were now in full voice, and when former Lions loanee Martyn Waghorn, who had only been on the field as a sub for eight minutes, became the first of three players to be red carded for kicking out at Dan Harding, the volume was cranked another notch.
Ed Upson saw a low drive held by Carson as The Lions patiently went about trying to prise that vital opening goal. The introduction of Gueye added extra impetus and Millwall's patience paid off handsomely on 74 minutes. Lee Gregory expertly held the ball up for Harding on the overlap, and the left-back's inviting delivery was met by Abdou, who had timed his run into the penalty area to perfection to power home a header - his first goal since April 2013 against Sheffield Wedsnesday.
Wigan were then reduced to nine players when Jason Pearce was shown a straight red card for a crude challenge on O'Brien by the corner flag, with Upson quickly following for his reaction as tempers began to flare.
It was now the 10 men of Millwall versus the nine of Wigan, and the visitors had no option other than to throw caution to the wind and push forward in a bid to grab a leveller.
McClean did well to work an opening with seven minutes remaining, but there was a collective sigh of relief from the home fans when the Wigan man's shot was deflected for a corner.
However it was The Lions, and super sub Gueye, who made the points safe in the 92nd-minute. Latching on to a long forward ball from Mark Beevers, the winger showed great control and composure to rifle home into the bottom right corner and secure the points.
Bookings: Gregory (29mins), Martin (53mins), Bailey (63mins), Beevers (67mins)
Sending off: Upson (78mins)
Scorers: Abdou (74mins), Gueye (90+2mins)
Wigan Athletic: Carson, Maguire, McClean, Pennant (Chow, 80mins), Kyung, Boyce, Bong, Perch, Pearce, Fortune (Waghorn, 52mins), Kvist (Ojo, 90+1min). Subs not used: Habsi, McCann, Barnett, Murphy.
Sending offs: Waghorn (60mins), Pearce (78mins)
Ref: S. Martin
Att: 8,494 (away 178)