A first Cottagers league goal from on-loan Roma striker Stefano Okaka and a fine headed goal from Brede Hangeland cranked up the relegation pressure on the struggling Latics.
Though without in-form talisman Bobby Zamora, Fulham started with the zest of a side full of confidence after their superb 2-1 Europa League victory over Wolfsburg.
The Cottagers created the first clear chance after five minutes when Thursday's European hero Damien Duff picked out Zoltan Gera, but his header was well held by goalkeeper Chris Kirkland.
Then Zamora's replacement David Elm found space in the box, but Kirkland was again equal to the effort.
However, the hosts should have had the chance to score from the spot after 20 minutes with the Fulham faithful livid at referee Mark Clattenburg for failing to award a penalty after Gera appeared to be sent sprawling by Titus Bramble.
But, after showing their defensive resilience, Roberto Martinez's side so nearly notched the opener just after the half hour when Paul Scharner's lob was cleared off the line by Hangeland.
There was no reprieve for Fulham though in the 34th minute when the Latics grabbed the lead through a half-volley from Jason Scotland that caught Mark Schwarzer out at his near post, after the hosts had allowed Marcelo Moreno to nod down for the former Swansea hitman.
Fulham drew level though less than two minutes into the second half when substitute Okaka flicked the ball past Kirkland with his first touch after good work down the left by the impressive Gera.
That leveller transformed Fulham and their improved second-half showing was rewarded in the 58th minute with Hangeland's towering header from a Duff corner finding the back of the net via Kirkland's outstretched hand and a post.
The Fulham fans claimed another penalty near the end when Clint Dempsey went down after a challenge by Bramble, but this time action replays showed that it was a clean tackle and two was enough for Fulham in the end.
Goalscorer Okaka handed manager Roy Hodson another injury headache though when he hobbled off with five minutes to go.
However, Zamora's apparent knock that ruled him out was not thought to be serious enough to make him a doubt for the European quarter-final second leg at Wolfsburg.