But Mourinho, writing for Telegraph Sport on Sunday, says that the striker should not be on the pitch on Tuesday because of a foul he committed against Aalborg in United's last group game.
Rooney made two poor challenges during United's 2-2 draw at Old Trafford that night but both went unpunished by French referee Laurent Duhamel.
However Mourinho, whose side went 12 points clear at the top of Serie A on Saturday, believes Uefa should have punished Rooney retrospectively for the fouls with a two-game suspension.
"Back in 2005 Uefa used TV evidence to suspend Michael Essien for a challenge that he made in the Champions League against Liverpool," he writes. "Against Aalborg, Rooney made a challenge that deserved punishment. But nothing happens. What is the difference between Michael Essien from Chelsea and Wayne Rooney from Manchester United? I don't think there is a difference."
United defender Nemanja Vidic is suspended for Tuesday's first leg at the San Siro for a foul he committed in the World Club Championship final but Mourinho is adamant that the Serbian centre-back should also have been banned for the return leg at Old Trafford on March 11.
"It is simple," he writes. "His elbowing in front of such a large audience deserved a two-game suspension. So he should not be playing in either leg. The rules are written."
Mourinho denies he is making these comments as part of any "mind games" with his counterpart Sir Alex Ferguson. "I think this game will only be played on the pitch," he says. "There will be no special words. When you are friendly with the opposing manager, like I am with Sir Alex Ferguson, it is more difficult to play those games."