'The Duke' pounced after 72 minutes to head home an inch-perfect cross from Andy Liddell to send the Premiership side packing in a repeat of last season's fourth round shock.
His two goals last season helped the first division leaders to a quarter-final spot and it could be that Paul Jewell's eager outfit could make history repeat itself.
They were always in control against a below-strength Fulham outfit but nothing should be taken away from them and indeed the victory margin could have been bigger.
Cottagers keeper Mark Crossley produced a string of fine saves to keep his side in the hunt as Wigan were rampant from the first half hour but ironically it was the visitors who almost went in front when Facundo Sava headed straight into the grateful arms of Wigan keeper John Filan.
A header from the same player then grazed the upright but they were isolated incidents in a Wigan-dominated first half.
Ellington gave notice of what was to come with a fierce drive early in the second period that once again tested Crossley, and then the outstanding Jimmy Bullard put Geoff Horsfield through only for Crossley to rescue his side once again with a fine save at the near post.
And as Wigan held on in the closing stages amazingly Crossley was the player who almost dragged his side level.
The Fulham keeper charged up field for a corner in the dying seconds and when the ball was headed out to him on the edge of the box he unleashed a stinging drive that his Wigan counterpart turned round the post for a corner.
But Wigan survived the late scare and now await the draw for the next round and there won't be a club in the land that will relish a trip to the JJB Stadium.
Wigan: Filan, Eaden, Breckin, Jackson, Kennedy, Liddell, Dinning, Bullard, McCulloch, Horsfield, Ellington. Subs: Walsh, Teale, Mitchell, Flynn, Roberts.
Fulham: Crossley, Leacock, Melville, Djetou, Green, Buari, Inamoto, Legwinski, Stolcers, Pembridge, Sava. Subs: Beasant, Boa Morte, Pratley, Rehman, Tom Davis.
Referee: A Kaye (W Yorkshire)