Rooney was brought on late in the game at the Friends Arena, by which point victory had been all but secured thanks to goals from Paul Pogba and Henrikh Mkhitaryan, before going on to lift the trophy after the final whistle.
But Mourinho dismissed speculation that the late substitution symbolised a final swansong for the 31-year-old, insisting that Rooney remains an "important player" at the club.
"Wayne Rooney was ready to play, he was a big option," Mourinho said afterwards. "But I didn't need to attack at 2-0.
"You have to control the game, you have to delay the changes, bring in players step by step.
"I told him yesterday that he could be the key man but he can perfectly be here next season.
"He is a very important player for us. If he stays next season I'd be very happy."
Having been reduced to a peripheral role under Mourinho this term, Rooney's future at the club remains the subject of intense speculation. The player has been linked with a number of clubs throughout the past season.
The Independent understands that a return to boyhood club Everton is the likeliest course of action for the player who is currently faced with the prospect of another season on the sidelines should he remain at Old Trafford.
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