The victory was just about deserved but Steve Bruce's Wigan will rue a failure to take their chances, particularly in the first half, as their much-vaunted strikeforce of Amr Zaki and Emile Heskey failed to trouble Fulham's defence.
But that was in stark contrast to Fulham's £16million pairing of Johnson and Bobby Zamora, who finally lived up their billing as the Cottagers claimed three points to lift them away from the drop-zone, while Wigan will be looking nervously over their shoulders having lost their last four games.
The match started at a frenetic pace, but it was Fulham who took the lead thanks to a goal that was remarkable for its simplicity.
Paul Konchesky was the architect, working well with Zamora to create space down the left and firing in a first-time cross that Johnson could not fail to convert.
The striker was clearly two yards offside, but the 27-year-old did not care as he revealed a T-shirt that said simply '100 League Goals' to mark his achievement, which came in his 290th league game.
Johnson had not scored since netting for Everton in a UEFA Cup tie against Fiorentina in March and the confidence surged through him as only Maynor Figueroa's last-ditch tackle denied him a second.
But Wigan wasted a glorious chance to equalise on the stroke of half-time. Zaki - the revelation of the Premier League campaign to date - swung in a gorgeous cross from the left, and Paul Scharner somehow managed to head over from six yards when it appeared easier to score.
The visitors had dominated the final 15 minutes of the first half but Fulham nearly doubled their lead on 48 minutes when Zoltan Gera saw his turn and shot strike the base of an upright with Chris Kirkland nowhere near it.
But Fulham scored a second goal they barely deserved through Johnson on the hour.
It was a goal that Bruce - a former centre-back - would have hated to see his side concede as Scharner lost concentration, allowing Johnson to run behind him and touch Jimmy Bullard's quick free-kick past the on-rushing Kirkland from a tight angle.
And after establishing a two-goal cushion, Fulham were happy to get through the final half-hour without any alarms as they ended their terrible run and set themselves up for what promises to be a testing trip to face Everton on Saturday.