The Red Devils confirmed the news this lunchtime, ending an amazing week, which included Rooney insisting United no longer matched his ambitions.
Yet after a staggering 24-hour period, and a demonstration by irate fans at Rooney's house in Prestbury last night, Rooney is now set to stay at Old Trafford.
"Sometimes, when you're in a club, it can be hard to realise just how big it is and it takes something like the events of the last few days to make you understand," said Sir Alex Ferguson.
"I think Wayne now understands what a great club Manchester United is."
"Wayne has apologised to me and the players," Ferguson told Key103.
"He will also do so with the supporters."
It barely seemed credible such a position could be arrived at so quickly. But the conciliatory nature of a holding statement from United last night suggested rapprochement was in the offing.
And, after consultation with the owners, who allayed his fears about the future direction of United, Rooney agreed to extend his contract, which will now expire in 2015.
"It's been a difficult week, but the intensity of the coverage is what we expect at Manchester United," said Ferguson. "I said to the boy that the door is always open and I am delighted Wayne has agreed to stay.
"I am pleased he has accepted the challenge to guide the younger players and establish himself as one of United's great players.
"It shows character and belief in what we stand for.
"I am sure everyone involved with the club will now get behind Wayne and show him the support he needs to produce the performances we know he is capable of."
Rooney recognises damage has been done, possibly inside the dressing room and certainly with the fans who have regarded him as one of their own since he first arrived from Everton in 2004.
He also understands the need to improve his form, which has suffered so badly since he sustained an ankle injury against Bayern Munich in March, the last time he scored a goal for his club in open play.
"I am delighted to sign another deal at United," he said. "In the last couple of days, I have talked to the manager and the owners and they have convinced me this is where I belong.
"I said on Wednesday the manager is a genius and it is his belief and support that have convinced me to stay.
"I am signing a new deal in the absolute belief that the management, coaching staff, board and owners are totally committed to making sure United maintains its proud winning history - which is the reason I joined the club in the first place.
"I am sure the fans over the last week have felt let down by what they have read and seen.
"But my position was from concern over the future.
"The fans have been brilliant with me since I arrived and it's up to me through my performances to win them over again."