Ten-men Rovers grabbed a dramatic last-gasp leveller after a game of high drama at the DW Stadium.
A late arriving Rovers were quickly out of the blocks, Yakubu giving them the lead inside two minutes. But a Jordi Gomez strike and a Gary Caldwell header saw the home side lead at the break.
Rovers' task looked worse when David Dunn saw red for a second yellow card, but Junior Hoilett took advantage of a hugely contentious corner kick from Morten Gamst Pedersen to head Rovers level.
Paul Robinson then took centre stage for the wrong and then right way. The Rovers number one at fault as Albert Crusat regained the lead for Wigan, the ball slipping under the 'keeper.
But with six minutes of added time played Robinson, up for a late corner, went in bravely for a header only to be kicked by David Jones in the face. Andre Marriner pointing to the spot.
Yakubu showed no sign of nerves as he stepped up to send Al Habsi the wrong way and secure a point for Steve Kean's side.
Ahead of the game Steve Kean made four changes from the side that pushed Chelsea all the way last time out.
The game came too soon for team captain Christopher Samba as he recovers from a hamstring strain, whilst a late hamstring injury saw Martin Olsson miss out.
Jason Lowe served his one-match ban after picking up five yellows, whilst the fourth change saw Mauro Formica drop down to the substitutes bench.
Those changes meant a reshuffled back four, Michel Salgado and Scott Dann returning from hamstring and calf strains respectively, Dann was partnered by Grant Hanley at centre half as Olsson's absence meant a return to left-back for Gael Givet.
The home side also made a host of changes, five in total as Roberto Martinez looked to reverse an eight-match losing streak.
Rovers may have been delayed in getting to the DW Stadium, but there was nothing slow about their start.
Just 90 seconds were on the clock when from a Paul Robinson goal-kick David Dunn nodded on, Steven Nzonzi helped the ball on towards Yakubu, and as Wigan captain Gary Caldwell missed his clearance the Rovers striker advanced to lift the ball over Ali Al Habsi and the ball crept into the back of the net.
If the home side were stunned, they certainly didn't show it as they hit back straight away. Rovers had already escaped a penalty shout when Morten Gamst Pedersen appeared to trip Victor Moses in the area, but on eight minutes the scores were level.
A ball into the Rovers box was well cleared by Grant Hanley, but as Jordi Gomez claimed possession, he took a touch before lashing the ball into the corner of the net. Paul Robinson was unsighted as Conor Sammon was stood in an offside position in front of the Rovers captain but the goal was allowed to stand.
It was a frantic start to the match with plenty of tackles flying, both Ruben Rochina and David Dunn both yellow carded for needless challenges in the centre of midfield.
Rovers came within a coat of paint from regaining the lead on 19 minutes. Morten Gamst Pedersen hugely unfortunate to see his 30-yard free-kick smack off the inside of the post and away to safety.
From the resulting Pedersen long throw it came through to Gael Givet but he snatched at the shot with his right foot and the ball flew over the bar.
A clash of heads between Victor Moses and Michel Salgado meant concern for the Rovers veteran, and although he returned after treatment, he wouldn't return at the start of the second half.
Just past the half hour and Wigan's turnaround was complete. Jodi Gomez sent a corner from the left into the area and as a static Rovers defence stood and watched, Gary Caldwell atoned from his earlier error to head into the back of the net.
Roberto Martinez's side continued to pose the greater threat. Only a vital block from Scott Dann prevented Conor Sammon from getting a shot on target, whilst Victor Moses twice fired over the bar when well placed.
Then deep into added time at the end of the first half Gomez was given time and space to shoot from distance, his effort whistling inches past Robinson's far post.
Rovers made a half time reshuffle with 17-year-old Adam Henley coming on to replace the injured Michel Salgado, a debut for the Welsh youngster.
Then Rovers' job was made all the more difficult after David Dunn saw yellow for a second time for a foul on Diame. The Rovers midfielder had lost possession, and in his bid to regain it his late lunge on Diame saw him felled from behind. Andre Marriner having no option but to issue the red card.
Wigan's Jordi Gomez was then perhaps fortunate not to see red himself, catching Gael Givet as the Frenchman cleared the ball, he stamped fully on the defender's foot, but only a yellow card was issued.
Givet looked in some considerable pain as he was helped to the sideline. Then a stretcher was called for as Rovers indicated a change, yet somehow Givet limped back onto the pitch.
The hour mark saw Rovers get back on level terms in hugely controversial circumstances.
Whether referee Andre Marriner thought Yakubu had taken a corner kick on the left remains to be seen but he looked away as Morten Gamst Pedersen dribbled the ball from the corner flag into the area before firing it across goal. Ali Al Habsi got a hand to the ball but only to divert it up for a gleeful Junior Hoilett who headed home from two yards.
Junior heads Rovers level
The Rovers players weren't complaining, and perhaps surprisingly, neither were the Wigan players.
That prompted a double change from the home side as Gomez and Sammon were replaced by Albert Crusat and Hugo Rodallega.
But it was Rovers who then spurned a gilt-edged chance to grab the lead once again. It stemmed from a 72nd minute block from Scott Dann, the ball rebounding forward for Ruben Rochina to feed Yakubu in an advanced position, taking the ball past Al Habsi he was all set to fire into the empty net until the timely interception from Steve Gohouri.
Two minutes later and Rovers were thankful for a point blank save from captain Paul Robinson. A Dave Jones cross from the left found Rodallega in front of goal but his first time shot was superbly kept out.
But just when it looked like Rovers had rode their luck and seen off the Wigan threat the home side grabbed a crucial third goal.
A long ball was sent towards the edge of the Rovers area, Hugo Rodallega rose to head down for Albert Crusat, his shot wasn't the strongest but it somehow crept under Robinson and into the back of the net.
It was a bitter blow for Rovers after the ten men did so well to get back into the game the way they did.
The drama certainly didn't end there when after six additional minutes, a late, late corner saw Paul Robinson come up. Morten Gamst Pedersen's inswinger was headed high and as the Rovers goalkeeper went to head the ball he was kicked by a high boot from David Jones.
For once Rovers were the grateful recipients of a last-minute penalty decision as Andre Marriner had no hesitation in pointing to the spot.
After a lengthy delay for treatment to Robinson it was left for Yakubu to hold his nerve and cool as you like he stroked the ball into the back of the net with Al Habsi diving in the opposite direction.
Cool as you like from Yakubu
Games at Wigan are never dull, but this might well have been the most dramatic of them all.
WIGAN ATHLETIC: Al Habsi, Gohouri, McCarthy, Caldwell (c), Moses, Gomez (sub Crusat 68 mins), Sammon (sub Rodallega 68 mins), Jones, Diame, Stam (sub McArthur 90 mins), Figueroa.
Subs: Pollitt (GK), Watson, Maloney, Lopez.
ROVERS: Robinson (c), Salgado (sub Henley 46 mins), Hanley, Dann, Givet (sub Roberts 90 mins), Rochina (sub Formica 84 mins), Nzonzi, Pedersen, Hoilett, Dunn, Yakubu.
Subs: Bunn (GK), Petrovic, Blackman, Goodwillie.
Booked: Gomez, Stam (Wigan), Rochina, Dunn, Nzonzi (Rovers).
Sent off: Dunn (Rovers).