Uwe Rosler was unable to halt Wigan's losing run as their maiden European campaign ended with a controversial 2-1 defeat by Maribor.
Former Manchester City striker Rosler took charge of his first Latics match having succeeded the unpopular Owen Coyle at the weekend.
Wigan's hopes of reaching the last 32 of the Europa League were hanging by a thread after a costly home defeat by Zulte Waregem two weeks ago that played a major part in Coyle's departure.
That left Rosler's side needing to win in Slovenia and hoping Rubin Kazan, who had already secured top spot in Group D, could beat Zulte.
The Russians did their bit with a 2-0 victory but, having been reduced to 10 men in the first half, Wigan were unable to prevent a sixth consecutive defeat.
The 1,000 travelling fans went from ecstasy to agony in three first-half minutes that all-but sealed their fate.
First Nick Powell won a penalty that Jordi Gomez converted in the 41st minute, but there was barely time to celebrate before Maribor were awarded a spot-kick of their own.
Chris McCann was deemed to have handled a shot, and referee Szymon Marciniak exacted further punishment by showing the midfielder a second yellow card.
Scott Carson pushed Dejan Mezga's penalty onto a post but the ball fell nicely for the same player to equalise.
Fourteen minutes after half-time, Zeljko Filipovic scored what proved to be the winning goal, drilling an unstoppable shot into the top corner.
The result gave Maribor not just their first victory over an English side but also a place in the last 32.
Rosler will now turn his attention to trying to halt Wigan's slide down the Championship when neighbours Bolton visit the DW Stadium on Sunday.
Rosler's favoured passing style was in evidence from the start but Maribor were the first to offer a shot on goal, and it was a good one, Filipovic almost beating Carson from 20 yards.
Callum McManaman was keen to show his trickery down the right and he whipped in a fine cross that would have provided Powell with a great chance had Soares Arghus not diverted the ball behind.
Wigan continued to increase the pressure and Gomez was extremely unlucky with a free-kick in the 36th minute.
The Spaniard was fouled 25 yards out and picked himself up to curl a shot against the near post.
It was therefore no more than Wigan deserved when Powell tumbled under pressure from Arghus and referee Marciniak pointed to the spot.
Gomez's penalty was central but goalkeeper Jasmin Handanovic dived over the top of the ball to give the Latics the lead.
However, they were guilty of switching off as Maribor responded immediately, and paid a heavy price.
Marciniak had set his stall out with early bookings for Roger Espinoza and McCann so, having decided the latter handled Damjan Bohar's shot, a red card was not a complete surprise although extremely harsh.
Rosler made a change for the second half, sending on Ben Watson, the man who won the FA Cup for the Latics, in place of McManaman.
Not surprisingly, the Slovenians offered a lot more in attack, with Damjan Bohar drawing a diving save from Carson at the near post before Ales Mertelj shot over.
Wigan were trying to hit Maribor on the break and they came close when Jean Beausejour crossed for Powell, but he could only guide his shot wide.
The pressure was growing, though, and, after Nusmir Fajic had shot wildly over the bar with only Carson to beat, the hosts took the lead.
James Perch gave the ball away in a dangerous area down the right but it looked like the chance had gone as a misplaced pass rolled out of the box.
But running onto it was Filipovic and this time his shot arrowed into the top corner.
Watson almost drew Wigan level after good work from Espinoza but his finely-struck effort from the edge of the box was well saved by Handanovic.
Maribor broke away and should have put the game to bed but Bohar rolled his shot past the far post with only Carson to beat.
It was a shocking miss, and a minute later the Slovenians were also reduced to 10 men when Mertelj was shown a second yellow for a foul on Gomez.
Wigan kept pushing for an equaliser and Leon Barnett and substitute Marc-Antoine Fortune came close.
A draw would have denied Maribor a place in the knockout stages but it was not to be and the home side celebrated their prize exuberantly.