Latics suffered a potentially devastating blow to their Championship survival hopes when Neeskens Kebano scored the winner in the dying seconds at Craven Cottage.
The visitors had produced a spirited and hard working display which deserved some reward but they came away from South West London empty handed.
Floyd Ayite had put the Cottagers ahead from close range on 25 minutes, but Latics fought back to draw level through Scott Malone’s own goal and then Michael Jacobs had given them the lead just before half-time.
Omar Bogle had a great chance to make it 3-1 early in the second half but keeper David Button saved well with his legs.
Denis Odoi then fired a superb 35-yard shot past substitute keeper Matt Gilks to draw the teams level before Kebano’s dramatic stoppage time winner.
Latics remain second bottom and are five points from safety with 16 games remaining. Fulham move up a place to ninth the table.
Warren Joyce made one change to the starting line-up with David Perkins replacing James Weir in midfield.
Fulham dominated possession in the opening half and went ahead after 25 minutes through Ayite after good work by Sone Aluko down the right hand side.
But Latics soon drew level under rather fortuitous circumstances.
Stephen Warnock’s cross was delivered into the corridor of uncertainty and with Omar Bogle pressurising Scott Malone the hapless defender put the ball into his own net.
Fulham tried to respond and they went close when Stefan Johansen fired a dangerous ball across the face of goal.
But in first half stoppage time Latics went ahead. Perkins found Max Power wide on the left and his low cross was turned home at the back post by Jacobs.
Substitute keeper Matt Gilks replaced the injured Jakob Haugaard at half time.
Bogle then had the best chance of the game on 53 minutes when Morsy put him through on goal but Button managed to save with his legs.
Aluko then tested Gilks and soon afterwards he crashed another shot onto the top of the crossbar.
Fulham were now camped in the Latics half and constantly probing for the equaliser. The visitors were struggling to gain any meaningful possession.
Loanee Jamie Hanson replaced Perkins after 65 minutes but Fulham continued to dominate.
The home team drew level in the 71st minute when Callum Connolly conceded a free-kick 35 yards from goal. Johansen side footed the ball to Denis Odoi, who produced a spectacular dipping drive to beat Gilks from 30 yards.
Latics had a rare chance when Jacobs got clear in the box and his curling shot was superbly tipped away at full stretch by Button.
Will Grigg replaced the tiring Bogle with four minutes of added time remaining.
Latics had been defending in numbers throughout and as the match moved towards the final whistle they had retreated even further and with almost the final kick of the match Kebano was in the right position to angle his effort past Gilks to devastating effect.
Latics had produced a spirited display which probably deserved at least a draw. But there was also the feeling that Joyce should have changed his system in the second half. Latics were defending too deep and inviting pressure and they suffered the consequences.
Playing Grigg and Bogle together upfront would have given Latics an outlet in the second half rather than leaving the increasingly isolated Bogle to fight it out alone.
With two strikers they would have posed a much greater threat and Fulham would have been reluctant to commit so many men forward.
Joyce’s reluctance to play Grigg and Bogle together is now starting to cost the team vital points.