The captain was dropped for the weekend's Premier League win over Leicester City before coming on as a late sub and was again a second-half change in the Europa League clash with Zorya Luhansk.
Rooney, although inadvertently, had a hand in Zlatan Ibrahimovic's 69th-minute winner after replacing Jesse Lingard two minutes earlier and his contribution greatly assisted United in recording their first win of the European season.
"Since the first minute we were waiting for the goal but it didn't arrive," Mourinho said.
"You never know what happens and Sergio Romero made a good save when the score was 0-0.
"I had good players on the bench to help change the game.
"Wayne Rooney gave us different positions and speed when the opposing team was getting tired."