Goal.com revealed the England international told team-mates he could soon leave the Premier League champions-elect after being left out of the Champions League quarter-final loss to Real Madrid in March - while PSG president Nasser Al-Khelaifi played down and director Leonardo rejected talk of a switch.
Rooney has fallen down the club's pecking order in recent months, with summer recruit and top goalscorer Robin van Persie becoming the focal attacking point at United - but his boss has rubbished the transfer speculation.
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Rooney is two-and-a-half years into a five-year deal at Old Trafford, signed following an infamous U-turn after calling United's ability to attract top players into question.
The England international was subbed against West Ham following an ineffectual 71 minutes as his side twice went behind before salvaging a draw, but Sir Alex insists the change was purely down to tactics.
"As far as taking him off the other night, it was simple; he wasn't playing as well as Shinji Kagawa was," the 71-year-old added. "In so many games Wayne Rooney is better than most players. But on the night Shinji was playing so well.
"The ironic thing was, when we were chasing a goal with 14 minutes left, I decided to put Chicharito on and Shinji made the second goal.
"I'd already given the fourth official the card, Chicha was standing on the touchline and then we scored the second goal. I think if I'd have changed my decision then we would have won it.
"Shinji was doing really well but unfortunately he came off. Chicha came on simply because you always think he'll get a chance in the game. At that point we wanted to win it and if you make decisions like that that mabye are not fair."