The Red Devils beat the Swiss outfit 3-0 at Old Trafford on United’s return to the Champions League.
Herrera, 28, started his first Premier League game of the season last weekend against Stoke but Mourinho dropped the Spain international last night.
And the United boss has confirmed it was a tactical move to axe Herrera from the squad, with Mourinho favouring Michael Carrick and Marouane Fellaini for spots on the bench.
"No reasons to be out," Mourinho said.
"We are playing only with two midfield players, with Matic and Pogba, who are playing really well and without reason to change.
"The only match we decided to play with three [Herrera] played, today we went back to two again.
"And I had on the bench [Michael] Carrick and [Marouane] Fellaini, which were also important players last season.
"We have a group of players who must be ready to play and not to play.
"Ashley Young was not on the bench in the last match and today he started the match and played 90 minutes.
"And the next match you can have another surprise of some player you think is going to play and is not going to play.
"It's the squad we have, I have to use the players and that's the life in clubs with squads of quality."
United are back in action on Sunday when the Red Devils face Everton on Sunday afternoon.
