Reports had claimed that the England forward had asked to leave the club but Rooney, his representatives and the club had previously refused to confirm those stories until Ferguson spoke out during a post-match interview following the 2-1 win over Swansea.
Rooney was absent from the squad for the match - Ferguson's final fixture at Old Trafford - and afterwards the United manager told Sky Sports: "I don't think Wayne was keen to play simply because he's asked for a transfer. 
"I think he wants to think things through in his mind; I think that's a good idea. 
"We're not going to let him go. I think he's maybe a bit frustrated that he's been taken off once or twice in the last few weeks."
Following their victory over Swansea, United were presented with the Premier League trophy, but some sections of the crowd jeered Rooney as he came forward to collect his medal before shaking Ferguson's hand.
Veteran United midfielder Paul Scholes, however, did start the match, with the 38-year-old making his final home appearance after he also confirmed that he would be retiring for a second time at the end of the season.