Rooney, who has two years left on his contract, told Ferguson two weeks ago he wanted to leave the club but the 27-year-old, who has two years left on his contract, was told he had to stay at Old Trafford.
A United spokesman confirmed to Press Association Sport: "Wayne Rooney is not for sale."
Moyes, who first gave Rooney his debut as a 16-year-old at Everton, will now have to tackle the fall-out of the current impasse between player and club.
On Thursday, sources close to Rooney made clear they, he and his representatives will adopt a wait-and-see approach to Moyes' appointment.
Rooney has been unhappy at being played predominantly in midfield, though with Robin van Persie in the team it looks unlikely that Moyes would alter the line-up significantly from Ferguson's first choice.
Rooney was also left on the bench by Ferguson for Real Madrid's visit in the Champions League round-of-16 game, a decision that irked the player.
It is now anticipated by Rooney's camp that United will make him an offer of a new contract but the level of his wages will be a decisive factor. Rooney is reported to earn around £250,000 a week on his current deal, and the club would be reluctant to increase it - and he would certainly not accept a pay cut.
Moyes and Rooney have had their differences in the past, particularly when the manager won substantial libel damages, which he donated to charity, over remarks about him in the player's autobiography. That has been smoothed over however and is no longer regarded as an issue in their relationship.
Meanwhile, reports on Thursday suggested that Rooney had removed 'Manchester United player' from his Twitter biography and replaced it with 'NikeUK athlete'. His representatives insisted no change had been made recently and it later emerged that a number of other Nike-sponsored players - including United team-mate Tom Cleverley - had made similar changes to their social media biographies some months ago.
- Sports & Recreation
- Wayne Rooney