The Columbian's header put Martin Jol's side on the road to three points at the DW and helps them continue their fine recent results against the Latics
After a decent opening spell from the home side, it was former Wigan striker Rodallega who broke the deadlock, sending a powerful header past Ali Al-Habsi from the impressive Dimitar Berbatov's inch-perfect cross.
And despite an improved second-half showing from Wigan in which they missed several glorious chances, winger Duff hammered a low drive into the bottom right-hand corner of the net to seal the three points for Fulham.
Arouna Kone pulled one back in stoppage time, but it was too little, too late for the Latics.
Wigan boss Roberto Martinez made two changes from the team that went down 4-0 at Manchester United last week. In came Ben Watson and fit again Jordi Gomez, with James McArthur dropping to the bench and top scorer Franco Di Santo out having picked up a calf injury in training on Friday.
Martin Jol, on the other hand, kept the faith with his starting XI from last weekend's 3-0 thumping of West Brom with two-goal hero Berbatov leading the line alongside former Wigan man Rodallega. Striker Mladen Petric made his return to the squad after injury.
And perhaps eager to end their recent hoodoo against Fulham, it was the home side who made the better start to the contest.
Fulham were struggling to maintain any concerted periods of pressure with Wigan the more committed and tigerish in midfield – Watson, in particular prevalent.
Referee Lee Probert was the unlikely man to discover just how tough both sides were in the tackle, taking a double challenge from Watson and Steve Sidwell - much to the mirth of the DW Stadium.
Slowly but surely however, the momentum began to swing in favour of Fulham.
Firstly, Sidwell's near-post flick from a Damien Duff corner was acrobatically cleared on his own goal-line by Jean Beausejour with Rodallega ready to pounce, before the increasingly influential Berbatov tried his luck from fully 30-yards – Ali Al-Habsi taking no chances to pat the Bulgarian’s swerving effort behind.
Wigan were struggling to get a foothold in the game after their bright start, and Emmerson Boyce wasted a glorious opportunity, heading fellow full-back Maynor Figueroa's pin-point left-wing cross wide.
And the home side were made to pay for their profligacy as Fulham took a 31st minute lead in a simple, yet elegant manner.
Berbatov, at the hub of all things positive in the first-half, lofted in a precision cross from the right and Rodallega timed his run to perfection to bullet a header past Al-Habsi, with celebrations limited out of respect for his former club.
Wigan responded well to going behind and were unlucky not to restore parity before the break when Beausejour's perfectly weighted left-wing cross was well met by Jordi Gomez - the Spaniard unfortunate to see his guided effort smash the crossbar and bounce away to safety.
Perhaps stung by their manager’s words at half-time, it was the home team that once again leapt out of the blocks the quicker in the second period with Gomez carelessly straying offside when unmarked.
Unlike the first 45 minutes, Wigan were converting their superior possession into chances and Kone should have done better than to fire straight at Schwarzer after racing clear.
But moments after Mauro Boselli passed up a gilt-edged chance to equalise for the Latics, Fulham sprang down the other end to double their lead.
With Wigan committing more and more players forward, substitute Bryan Ruiz's hard work paid dividends in eventually switching the ball across the penalty area to Duff, who sent a rasping low drive beyond Al-Habsi.
Again the home side tried to hit back quickly and Fulham had Schwarzer to thank for preserving their two-goal cushion, the Australian tipping Ivan Ramis' close-range header onto the crossbar from Beausejour's free-kick.
And as the game drew to its conclusion, the west London outfit came close to extending their winning margin on the break, with the tiring Berbatov unfortunate to see his instinctive finish pushed wide by Al-Habsi.
Kone eventually converted a Wigan chance after a goalmouth scramble to pull a consolation back for the hosts, but it ultimately proved too little too late as Fulham moved into the top four for the time being, leaving Wigan to rue missed chances as their search for consistency continues.