The England international will stay at Old Trafford until 2019, having signed a new deal to replace his old one, which was due to expire at the end of next season.
Rooney's future had been the subject of much debate in the close-season, after previous manager Alex Ferguson revealed the striker had asked to leave the club.
The 28-year-old is currently fourth on United's list of goalscorers with 208 goals in 430 appearances, and is honing in on Bobby Charlton's all-time record of 249.
"Wayne has been the best player in England since I put him into the Everton first team in 2003," he told the club's official website.
"Since becoming United manager in July last year, I have enjoyed working with him and seeing just how he has developed his incredible talent.
"With his ability, his experience and his desire to succeed, he is a vital part of my plans for the future and I'm absolutely thrilled he has accepted the challenge.
"I said last July that Wayne has an outstanding chance to be a true legend of this club's long and rich history. He is just 42 goals away from overtaking Sir Bobby (Charlton) our record goalscorer and becoming the first United player to hit 250 goals for the club.
"These opportunities only come to special players and I'm confident Wayne will set a new record that will take decades to reach. These are really exciting times for everyone connected with the club."
