Mourinho opted to start both Ibrahimovic and Lukaku for the first time in the 2-2 draw with Burnley on Boxing Day.
But the veteran Swede was subbed at half time after a poor first half display.
He said: "It can happen but I think to happen they need both to be in their best moment and they're not.
"One is not, because the situation in his team didn't allow him to have any rest and he's giving absolutely everything in every minute and we just manage to give him a little rest in cup matches and even then he was on the bench for emergency situations.
"The Champions League was about the same. We had to fight until the last match for qualification.
"Zlatan is a man with an incredible injury, an injury that a 20-year-old man or young man would suffer, imagine a man 36-years-old and so many miles in high level football, so it's not easy.
"We did that against Burnley, we will do that in some more matches if we need to do, but for both to play together we need them to be at their best level."