The goals all came in the first period with Rooney finding the net midway through the half and just before the break after defender Gary Cahill had put the visitors ahead with his first international strike.
"It was very important to win here," England coach Fabio Capello told reporters. "We played a really good game and prepared really well."
England, playing in unfamiliar dark blue shirts and light blue shorts, went in front when Bolton Wanderers defender Cahill converted a pass from Gareth Barry after 13 minutes.
Cahill was a target for Arsenal and Tottenham Hotspur before the transfer window closed earlier this week.
"It's been a crazy week, a difficult week mentally," he explained. "But once the window shut I knew I was staying so I'll get my head down and work hard for Bolton and my country."
Rooney, who has been on fire for Manchester United this season, made it 2-0 with a firm header from Stewart Downing's right-wing cross.
The unmarked Rooney then tapped the ball into an empty net from close range following a fine solo run by Theo Walcott and a precise right-wing centre from Ashley Young in first-half stoppage-time.
Capello's side top the group with 14 points from six games, three ahead of Montenegro who lost 2-1 to Wales on Friday. Bulgaria remain fourth with five points.
England's victory could have been even more emphatic as they dominated throughout.
LAMPARD LEFT OUT
Downing headed against the post from a delightful cross by Young and home keeper Nikolay Mihaylov did well to parry Scott Parker's stunning drive.
Chelsea's Frank Lampard, who had 86 caps at the start of the day, was left out by England in a competitive match for the first time since 2007 and the decision was vindicated as Parker and Barry shone in midfield.
Lampard eventually came on for Barry with 10 minutes left.
"I decided on Barry instead because I saw the last game he played and he was in good form," added Capello.
"Frank is always a really important player for the national team. He is getting better but he is not on top form at this moment."
Walcott escaped the offside trap but could not find the fourth goal as his 18-metre shot went wide with only Mihaylov to beat.
Defeat virtually knocked Bulgaria out of the competition as Lothar Matthaus's team failed to score in a third consecutive home game in the group.
"We all saw the difference between the two teams," said former Germany playmaker Matthaus.
"We tried to create some scoring opportunities but England played very well."
