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.
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.
