Ten-man Rovers suffered stoppage time heartache as they slipped to a narrow 2-1 defeat at the DW Stadium.
For an hour Rovers worked tirelessly after Grant Hanley had been sent off for violent conduct, but they were undone by two late set-pieces.
Rovers started well and deservedly took the lead when Tommy Spurr scored his first goal for the club when he fired home from close range on eight minutes.
Gary Bowyer's side looked in control, but the red card on 30 minutes of the Rovers captain for an altercation with Nick Powell saw the tide turn in the home side's favour.
Wigan as you'd expect, saw plenty of the ball after that but Rovers saw out the first half and were battling hard to keep their lead when Grant Holt's header deflected into the back of the net on 69 minutes.
With the Latics pouring forward in search of a winner Rovers almost re-took the lead on 89 minutes but Josh King's bullet of a shot was a whisker over the bar.
Two minutes into five additional minutes at the end of the game and Rovers' hearts were broken, as one free-kick too many was sent into the box and Emmerson Boyce glanced home off the upright.
It was harsh on Rovers as to a man they worked their socks off, but they can be proud of the way they acquitted themselves.
Gary Bowyer was forced into changing a winning side for the match at the DW Stadium as captain Scott Dann failed to recover from the groin injury sustained in the 1-0 win over Watford.
That meant a first start for summer signing Matt Kilgallon, slotting alongside Grant Hanley who wore the armband for the game.
The home side made two changes from their Europa Cup win over Maribor on Thursday night as Emmerson Boyce and Callum McManaman made way for Thomas Rogne and James McClean.
Rovers were quick out of the blocks at the DW Stadium, their bright start rewarded as they took the lead inside eight minutes.
Following a foul on Leon Best Rovers were awarded a free-kick which Tom Cairney fired into the box, Best made himself a nuisance as both the striker and Wigan 'keeper Scott Carson went up for the ball, Carson couldn't hold and Tommy Spurr was on hand to fire through the crowd and into the back of the net.
The defender couldn't hide his delight as he celebrated his first goal for the club.
The home side responded as James McArthur curled a shot just wide, whilst Corry Evans send a dipping narrowly off target.
Played in a lively atmosphere, there was a good intensity to the play as both sides looked to press at every opportunity.
A deflected James McClean shot was well claimed by Kean, then straight up the other end Evans saw his goal-bound strike brilliantly blocked. Tom Cairney could only find the gloves of Carson after making room for an effort at goal.
Just past the half hour came the talking point of the first half as captain Grant Hanley saw red for violent conduct.
The Scottish international brought the ball out of defence before finding Tommy Spurr, but under pressure from Wigan striker Nick Powell, Hanley was adjudged to have caught the forward with an arm and referee Stuart Attwell issued a straight red card.
That prompted a sustained spell of pressure for the final 15 minutes of the half. Kean saving well after Jordi Gomez fired through the crowd, before the young stopper claimed a Powell header from James Perch's centre.
With a man shy Leon Best eventually had to make way, but not before the striker made an important defensive block to keep out a goal-bound header from Leon Barnett.
Lee Williamson came on to replace the striker, in a reshuffle that saw Jason Lowe go to centre half alongside Matt Kilgallon.
Despite being a man down it was Rovers who were the side looking for the second goal at the start of the second half.
After a Spurr long throw dropped to Lee Williamson outside the area, his shot deflected as far as Jordan Rhodes who spun and struck goalwards, the ball hit a the flailing arm of Ben Watson. To a man the 3000 Rovers fans and players appealed but Attwell was unmoved.
Wigan went back in search of an equaliser but a break by Josh King saw Rovers threaten once more, Cairney playing the ball to Evans but his shot was blocked.
Owen Coyle responded by throwing on an additional striker with Grant Holt making his return from a knee injury, a positive change as he replaced central defender Thomas Rogne/
Urged on by Gary Bowyer the Rovers fans were willing their side to sustain the pressure, Kean making a fingertip save to from Holt's drilled cross, Lee Williamson on hand to clear.
For some 40 minutes Rovers had withstood the Wigan pressure but on 69 minutes the home side were level. A Jordi Gomez corner found it's way to Grant Holt who nodded goalwards, the ball ricocheting off Tommy Spurr and trickled into the back of the net.
It was heartbreaking to concede in such a manner, but Rovers didn't let their heads drop despite the increase in pressure. Jean Beausejour and James McClean both going close as the game entered the final ten minutes.
Further chances came and went from the home side before Josh King almost claimed the points for Rovers. Cutting inside onto his right foot he fired goalwards, his shot had beaten Carson but the ball flew inches over the bar.
Five additional minutes were shown but Rovers conceded a second after two of them. They'd defended ball after ball into the area all afternoon but as Ben Watson delivered, Emmerson Boyce stole in to break Rovers' hearts.
Games between these two sides are rarely dull affairs, on this occasion Rovers were on the wrong end of this climatic conclusion.
WIGAN ATHLETIC: Carson, Shotton (sub Boyce 62 mins), Rogne (sub Holt 57 mins), Watson, McClean, Gomez, McArthur (sub McCann 83 mins), Powell, Beausejour, Perch, Barnett.
Subs not used: Nicholls (GK), Espinoza, Garcia, Dicko.
Goals: Holt 69 mins, Boyce 90+2 mins.
Booked: Shotton, Perch.
ROVERS: Kean, Kane, Hanley (c), Kilgallon, Spurr, Cairney (sub Taylor 84 mins), Lowe, Evans (sub Marshall 90+3 mins), King, Best (sub Williamson 41 mins), Rhodes.
Subs not used: Eastwood (GK), Marrow, Morris, Judge.
Goals: Spurr 8 mins.
Booked: Kane, Cairney, Kean, Rhodes.
Attendance: 16,996 (3630 Rovers fans)