Rooney's controlled 79th-minute finish put United 10 points clear atop the Premier League, with Manchester City playing Liverpool on Sunday, and continued the striker's renaissance in red after an unconvincing first half of the season.
With the match evenly balanced and both sides pushing for a winner, Rooney capitalised on a misjudgement by Fulham's Philippe Senderos before curling a shot around Aaron Hughes and into the bottom corner.
There was an effortless swagger in Rooney's finish that suggests he's just getting started. Rooney scored both goals in United's win at Southampton in midweek and also netted in their 4-1 FA Cup defeat of Fulham a week ago. Five goals in eight days says everything you need to know.
Also encouraging for United is Rooney's ever-improving understanding with Robin van Persie. Van Persie endured one of his poorer games against Fulham, but there was still some fine link play to behold between the Dutchman and a man who has spent most of the season in his shadow.
Elsewhere for United, David De Gea answered his critics with a clean sheet that included a brilliant diving save from Bryan Ruiz. The goalkeeper put in an accomplished performance that will have pleased his manager no end.
Fulham were left to rue not taking their chances. Martin Jol's team matched United's total of 16 shots, with six on target, but failed to break down an organised United defence who were well-marshalled by Rio Ferdinand and Jonny Evans.
This was far from the runaway victory United enjoyed against Fulham in the FA Cup, but another three points gained moves Ferguson's team closer still to a 12th Premier League title of his reign.
Ironically, United's great rivals Liverpool can help them move them even closer by denying Manchester City victory on Sunday.