Rooney, who entered the pitch in the 67th minute, made an immediate impact in the game as two minutes later his scuffed shot was headed home by Zlatan Ibrahimovic for the only goal of the game.
Following the match, Mourinho revealed that Rooney had jokingly claimed his effort to be an assist.
He said: "He was laughing and said he made a great assist.
"He gave me what the team needed at the time, which was a second presence in the box.
"He's more of a striker than Juan [Mata], and Juan went more to the right-hand side [when Wayne came on].
"We started the game with a very good team, and I also had players on the bench to give me solutions for everything."