His header set Roy Hodgson's men on their way to victory over Poland at Wembley which ensured they topped Group H. The captain, Steven Gerrard, scored a second two minutes from the final whistle.
Rooney's 41st-minute breakthrough was brilliantly created and executed after a patient England build-up gathered pace when Leighton Baines crossed for the Manchester United striker, who nodded the ball down and wide of keeper Wojciech Szczesny.
The match was played on a knife-edge as anything other than a win would have consigned England to a potentially difficult two-legged playoff tie, with group rivals Ukraine cruising to an easy win over San Marino.
But Gerrard sparked English celebrations in the 88th minute when he burst into the area, cut inside and poked the ball past Szczesny.
Later Rooney said: "We knew it was going to be a tough game, they had a couple of breaks and could have scored but we played some great stuff. Getting the goal gave us some belief, the confidence to go on. We believed we could win and then Stevie's goal has seen us qualify."
He added: "A big part of our preparation was being patient. We knew we may even have to win the game in the last 10, five minutes. We kept our focus and deserved to win.
"We had a great focus and belief going into these two games. That came out. We have some fantastic young players, experienced ones like Steve, Frank [Lampard] and me, we have a good blend, are looking forward, excited and these are good times for England."
Captain Gerrard, who led from the front as he has done throughout an unbeaten qualifying campaign, added: "We started really well. The big lesson is to play better in the second half. Against better teams we might get hurt. We need to keep the ball better. But what we have shown is, when the going gets tough, we don't concede goals."
England have faced some criticism during the campaign, but Gerrard said: "Since I made my England debut there has always been criticism from the outside. What it makes you do is work harder to prove people wrong.
"We have a great togetherness, are there for each other and proved we can perform under pressure."
Hodgson said: "I am delighted for the players. We played some sensational football in the first half and in the second, when the Poles had not so much to lose, we dug in, worked hard to control them."