Darren Fletcher was the first to benefit as he ran on to an angled ball only to slot wide of the target.
The recalled Ryan Giggs was the next to profit from a Berbatov ball but he saw his left-foot spectacularly saved by Brown.
A minute later and keeper Brown was somewhat harshly picking the ball out of the net.
The Blackburn stopper, standing in for the injured Paul Robinson, collided with Vidic as he went to try and collect a Rooney cross and the ball was headed in by Brown at the back post.
While the United defender celebrated only his third goal for the club, his namesake in the Blackburn nets vented his fury at referee Steve Bennett for allowing the goal.
I will be fine for England duty - Rooney
Rooney could have added a second after another defence-splitting pass from Berbatov, but Brown came out quickly to narrow the angle and save with his left hand.
Other than a Matt Derbyshire shot that was saved by Edwin van der Sar and a Brett Emerton effort that flashed wide, there was little for Ince to be positive about in the opening half.
And his half-time team talk failed to alter the flow of the game as United dominated, with Berbatov setting up Ronaldo only for him to drag his shot wide shortly after the break.
For an hour the Portuguese winger had looked a shadow of his former self as he continues to battle back from injury.
But then he received the ball on the right and exploded past Martin Olsson before squaring for Rooney to curl a shot past Brown.
We deserved to win the game - Phelan
Rooney could have had a second when he ran through before lobbing Brown, only to see it land on the roof of the net, before the Rovers keeper did brilliantly to deny Berbatov a deserved goal with his feet.
Blackburn had a chance to pull one back but Emerton's volley was blocked by Vidic.
Ronaldo slid a shot past the post and then set up Tevez to fire against the upright as United kept going until the end.
Ince's side simply had no answer as he was handed a lesson from his former boss, but on this form few teams in the Premier League could have lived with United.
Blackburn boss Paul Ince on the controversial opening goal: "I wouldn't say it cost us the game but it was 0-0.
"If the referee can't see it then he shouldn't be a referee. If not then the linesman should see it - it was a diabolical decision.
"They (United) were absolutely awesome, they are a fantastic side and champions of Europe but decisions change games."
Manchester United manager Sir Alex Ferguson: "We said before the game this is one of most difficult grounds to come to, but it was a really emphatic performance.
"The confidence was outstanding and everyone was on song. Everyone's use of the ball was spot on and we controlled the match.
We missed a lot of chances and it could have been a big score for us."
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