Many believed he had been dropped by the Portuguese boss, but he confirmed it was simply a case of resting the forward before a busy schedule of fixtures.
Speaking about Rooney, Mourinho insisted he wanted him to be fit for the Watford fixture.
“Wayne has played every game since the start of the season,” he said.
“He has also played 90 minutes for England and he played 90 minutes last weekend and I want him to be fresh for the next match.
“In the position he plays I have lots of solutions.”
Rooney has received some harsh criticism this season, although some of his performances have been below-par, he has still tried to give everything he can in each game.
The Englishman now has some time to rest as it’s clear Mourinho wants him to stay fit for the bigger Premier League fixtures.
The Europa League will also give Mourinho the opportunity to give game-time to players who have seen little or no action so far this season.