United officials buried a time capsule near the tunnel before kick-off to mark 100 years at Old Trafford and Rooney etched his name deeper into the club's rich fabric with another unstoppable display aided by the silky Dimitar Berbatov.
The England striker is on course to surpass the 42 goals scored by Cristiano Ronaldo in the 2007-08 season.
On a day when United laboured to answer Saturday victories for Chelsea and Arsenal which dropped them down to third, Rooney provided the spark with a performance that illustrated why his nation's World Cup hopes rest so squarely on his shoulders.
His instinctive first goal, 30 seconds into the second half, punctured Fulham's resistance and his second with six minutes remaining settled a few jitters against a dogged London side for whom Bobby Zamora fluffed two great chances.
To cap his afternoon Rooney's raking pass instigated a move that ended with Berbatov adding a third goal as United, bidding for a fourth consecutive title, moved to 66 points with eight games remaining, two ahead of Chelsea and Arsenal.
"I think Wayne can go over 40 goals," Berbatov told MUTV. "We have plenty of games till the season is over so I wish him luck and we're all going to help him to go over the 40 line.
"I think he is the best in the world. He is still so young and has chances to become even greater. Like I've told him many times, stay healthy and you can achieve everything."
In Sunday's other match, fifth-placed Manchester City needed a superb stoppage-time equaliser by Adam Johnson to earn a 1-1 draw at Sunderland which left them two points behind Tottenham Hotspur in the battle for fourth spot.
SLOW START
Rooney devastated AC Milan in midweek but hardly got a kick during the opening 20 minutes at Old Trafford as Fulham stifled the home side, although he did burst into life with a snap shot that was well saved by Mark Schwarzer.
Fulham, beaten in the Europa League by Juventus on Thursday, could have taken the lead when Zamora left United's central defensive duo of Rio Ferdinand and Nemanja Vidic for dead but his attempted lob cleared the crossbar.
A frustrated Rooney went off at halftime complaining about a penalty that was not awarded but he lifted the mood straight after the re-start when he found space in a congested area to beat Schwarzer with a side-foot finish.
Zamora wasted another chance by delaying too long when clean through, allowing Vidic to make a block, and Rooney sealed the points with a sweeping right-foot finish after great wing play by Berbatov.
The Bulgarian then headed in a Park Ji-sung cross to reach double figures for the season.
A rip-roaring second half at the Stadium of Light saw Manchester City lay siege to the home goal as they sought to make amends for a dismal opening 45 minutes in which Kenwyne Jones headed Sunderland in front.
Sunderland keeper Craig Gordon made several outstanding saves but could do nothing when Johnson curled a left-foot shot into the top corner just past the 90-minute ma
