Chelsea were unsuccessful in their attempts to sign Rooney ahead of the current campaign and manager Mourinho is aware United have no desire to sell a prized asset to a domestic rival.
However, the Portuguese's suggestion that Rooney, whose contract ends in 18 months, could move abroad at the end of the season has been rejected by Moyes.
The United boss said: "I can only tell you that I disagree - although he will go to Brazil (with England for the 2014 FIFA World Cup)."
Moyes refused to criticise Mourinho, who he will come up against on Sunday at Stamford Bridge, but made it clear he would not comment on players at opposing teams.
"Everybody has their style. I wouldn't talk about other managers at other clubs and I wouldn't talk about other players at other clubs," added the Scot.
"I can't tell you what his motivation is but only time will give you an answer about Wayne.
"The club will deal with that - they will do all they need to do, no question."
Mourinho had earlier said: "Manchester United made it clear in the summer they don't swap or sell players to their direct rivals. They were clear in the way they approached the Rooney situation.
"I think maybe this summer they will try to sell to a non-direct rival. But they were very clear (about not selling to Chelsea)."
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