Rovers goalkeeper Jason Brown felt he was blocked off by Nemanja Vidic when Brown nodded home Rooney's first-half cross.
But there was no debating the second as Rooney clinically applied the first-time finish to Cristiano Ronaldo's cut-back.
Earlier, Arsenal's bid to go top of the table foundered at Sunderland but they were lucky to escape defeat at the Stadium of Light as Cesc Fabregas' 93rd-minute header salvaged a 1-1 draw.
Having been beaten by Hull last week, the Gunners have now dropped five points in two matches - although the result was enough to take them third.
Arsene Wenger's side appeared to have been beaten by Grant Leadbitter's stunning 86th-minute strike.
The midfielder picked the ball up 25 yards out and smashed a shot in off the underside of the crossbar.
Only minutes earlier Craig Gordon had saved at point-blank range from Robin van Persie, who had a goal chalked off just after half-time.
Theo Walcott cut the ball back from the right byline for the Dutchman to stab home but the England winger was ruled to have taken the ball out, although television replays appeared to suggest he had kept it in.
Spain midfielder Fabregas rescued the Gunners with a close-range header from a corner in the third minute of added time.
Former Arsenal striker Jeremie Aliadiere snatched victory for Middlesbrough at Wigan with a goal in the 89th minute.
A game of very few chances appeared to be drifting to a goalless conclusion when Stewart Downing nodded down a right-wing cross on the edge of the penalty area and the Frenchman fired home.
West Brom's match at home to Fulham was also a game of few chances but the hosts prevailed 1-0 thanks to Roman Bednar's solitary strike in the 61st minute.
A left-wing corner produced a scramble in the visitors' penalty area and when the ball reached Bednar he stabbed home from three yards.
He had a chance to double the advantage seven minutes later but was hustled out by Aaron Hughes as he closed in on goal.
Clint Dempsey had a good chance to equalise in the 70th minute when Jimmy Bullard picked him out unmarked but he diverted his header wide from 12 yards.
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by espnstar.com/football/premier-league/news