Mourinho said he wanted to keep his 30-year-old captain Rooney fresh for Sunday's league game at Watford.
"He (Rooney) has played every game since the start of the season. He has also played 90 minutes for the England team," Mourinho said.
"I want him to be fresh for the next Premier League match. In the position he plays, I have lots of solutions and people that it has been really hard to have a chance."
Henrikh Mkhitaryan and Jesse Lingard, who were taken off in the first half of United's 2-1 defeat by Manchester City in the league on Saturday, have also missed out on the trip to Rotterdam.
Timothy Fosu-Mensah was included in the squad as key defenders Luke Shaw and Antonio Valencia were also left out.
Mourinho said striker Marcus Rashford would start for the first time this season while Memphis Depay, Ashley Young and Michael Carrick have also been included in the 20-man squad.
(Reporting by Ian Rodricks in Bengaluru; Editing by Ian Chadband)
