Rojo suffered a serious knee injury against Anderlecht in April - the same fixture that saw Ibrahimovic sustain a similar problem - and the Argentine defender did not return to the first-team fold until the Champions League game with Basel on Wednesday.
However, despite playing one game fewer than both Ibrahimovic and Pogba, who has recently been recovering from a hamstring injury, Mourinho has hinted that Rojo is more prepared to play 90 minutes than his teammates.
The 54-year-old told reporters: "He played very well. We have to see how he is today and there is no more injury in the frame, but fatigue, maybe he feels a little bit. But to be honest, Zlatan returned before him, Pogba returned before him but he was in better condition than the others.
"He didn't return before because, during the last period of his recovery, we had all of the central defenders ready to play, so we didn't need to push him, we gave him more time to prepare."
Rojo will compete for a starting role with Chris Smalling and Victor Lindelof for the Premier League fixture with Brighton & Hove Albion.