Latics failed to regain top spot in the League One table after a below par performance at play-off chasing Portsmouth.
Both Blackburn and Shrewsbury secured three points on Easter Monday but Latics slipped down to third spot following the 2-1 defeat at Fratton Park.
Former Pompey manager Paul Cook will be disappointed that his charges never really got going in front of the TV cameras.
The hosts went ahead when Brett Pitman converted from the penalty spot after Dan Burn was adjudged to have fouled Ben Close on the edge of the area.
Early in the second half Pompey doubled their lead when Jamal Lowe produced a neat finish after Latics had failed to clear a low cross from the right hand side.
When Latics replaced the ineffective Gavin Massey and James Vaughan with Ryan Colclough and Will Grigg they started to create more opportunities.
Grigg forced a superb save from Pompey keeper Luke McGee before he pulled a goal back on 89 minutes with a fine header from Gary Roberts’ pinpoint cross.
Despite Latics’ late pressure Pompey held on to move level with six-placed Charlton in the play-off places.
Credit to Pompey for a resolute performance but Latics just weren’t at their best on the day.
Paul Cook made two changes from the team which defeated Oldham Athletic with Massey and Vaughan replacing Colclough and Grigg.
It was a scrappy opening with neither side gaining the upper hand.
Latics went closest when Max Power’s 25 yard low strike was turned around the post by McGee.
Latics had a couple of half-chances as first Michael Jacobs tried an acrobatic overhead kick from Dan Burn’s knock back and then Massey’s cross from the right-hand side was just too strong for Vaughan at the back post.
Chey Dunkley then headed narrowly wide from a Power cross before Vaughan had a great opportunity to put Latics ahead from the centre of the penalty area but he scuffed his shot wide.
But five minutes before the break a rare Pompey attack resulted in them taking the lead.
Dan Burn challenged Ben Close on the edge of the area and referee Tim Robinson controversially awarded a penalty.
Brett Pitman converted the spot-kick to give Pompey a surprising half-time advantage.
But matters got worse for Latics ten minutes into the second half when a somewhat incongruous low cross from Nathan Thompson on the right hand side evaded Callum Elder and found Lowe who turned in front of Burn and finished expertly at the near post.
Latics were stunned by the setback but they still weren’t making any headway until Colclough and Grigg replaced Massey and Vaughan on 66 minutes.
Colclough had a great chance after good work by Nathan Byrne but the winger somehow miscued his shot and it diverted off a defender for a corner.
McGee then produced two magnificent saves to deny Latics.
First he denied Nick Powell with a superb reaction save pushing the ball onto crossbar from close range after the midfielder had evaded several defenders challenges.
Then ten minutes later he denied Grigg at close range with an instinctive save diving to his left after a great move involving Byrne and Jacobs.
Grigg wasn’t to be denied however and on 89 minutes he pulled a goal back with a fine header from former Pompey player Gary Roberts’ pinpoint cross.
With five minutes of added time it was a breathless period as Latics went in search of the equaliser with a succession of dangerous crosses. But the hosts held firm and Latics suffered a rare defeat in League One.
Too many of Latics players had had an off day and manager Cook will expect much improved performances in the final eight games of the season as they go in search of automatic promotion.