Hugo Rodallega opened his Fulham goals account against the club he left in the summer to set Martin Jol's side on their way to a first away win of the season in the Premier League.
It is the second campaign in a row the Cottagers have broken their away duck at the DW Stadium, and the result lifted Fulham into the top four, at least until tomorrow.
Rodallega deservedly broke the deadlock in the 31st minute with a goal created by the excellent Dimitar Berbatov, and Damien Duff added a second goal midway through the second half before Arouna Kone scored in injury-time for Wigan.
The main talking point of the early stages was an unfortunate moment for referee Lee Probert, who was the unintended victim of a full-blooded challenge between Steve Sidwell and Ben Watson.
The referee was well and truly floored and there was a lengthy delay while he received treatment, although he did see the funny side, waving a red card in jest.
When play resumed, it did not take long for Fulham to get on top and three times they went close to taking the lead midway through the first half.
First a dinked cross from Berbatov was headed straight at Ali Al Habsi by Rodallega before Jean Beausejour acrobatically cleared Chris Baird's header from in front of his post.
Berbatov then drew a scrambling save from Al Habsi, and in the 24th minute the Bulgarian went close again with a wobbling shot that the Wigan goalkeeper was grateful to push over the bar.
The home side created their best chance a couple of minutes later, Maynor Figueroa crossing for a diving Emmerson Boyce at the far post but he headed wide.
It was no surprise that Berbatov was the creator of the opening goal, the striker building on his two goals against West Brom last weekend by expertly picking out the head of Rodallega.
The Colombian had been booed by the home fans earlier on but he earned their applause when he declined to celebrate his bullet header right in front of them, and he was given a warm reception when he was substituted late on.
That gave Wigan some much-needed urgency and Jordi Gomez was unlucky not to equalise in the 38th minute when he met Beausejour's cross perfectly but saw his left-footed shot hit the underside of the bar and bounce down just in front of the line.
The hosts began the second half brightly and Boyce's cross was headed just wide by Watson before Kone spurned a glorious chance.
The striker was played clean through but took a slightly heavy touch and could only poke his shot straight at Mark Schwarzer.
Both managers made changes, Bryan Ruiz replacing Alex Kacaniklic for Fulham while Mauro Boselli was given his chance by Roberto Martinez in place of Gomez.
Ruiz made an immediate impact, forcing a diving save from Al Habsi with a 20-yard free-kick after Rodallega had been sent tumbling by Gary Caldwell.
Wigan had certainly had their opportunities and in the 65th minute the ball fell for James McCarthy on the edge of the box and he draw a scrambling save from Schwarzer.
Boselli was first to the rebound but the Argentinian, still looking for his first Premier League goal two years after first joining the club, could only guide the ball wide.
The visitors made Wigan pay with their second goal three minutes later, Ruiz doing brilliantly to hold off the home defence and tee up the unmarked Duff for a clinical finish into the bottom corner.
Still the Latics plugged away and they would have pulled one back in the 73rd minute but for the fingertips of Schwarzer, who kept out Ivan Ramis' header with the help of the bar.
Martinez made his last throws of the dice, sending on Ryo Miyaichi and Callum McManaman, but it was Fulham who were next to threaten another goal, Berbatov denied by an accomplished save from Al Habsi.
Wigan did find the net eventually, Kone with a fine turn and shot, but, with only two minutes of injury time remaining, it came too late for the hosts.