Ferguson, taking charge of United for the final time at Old Trafford before retiring, dropped a bombshell by leaving Rooney out of the matchday squad.
And later he gave his reasons, telling Sky Sports: "I don't think Wayne was keen to play simply because he had asked for a transfer.
"He wants to think it through in his mind, which is a good idea."
Although Ferguson is standing down, to be replaced by Everton boss David Moyes, he insisted Rooney would not be allowed to leave the Barclays Premier League champions.
"We are not going to let him go but he is a little bit frustrated at being taken off once or twice in the last few weeks."