"It's time for Jones and Smalling to be fearless, to risk", Mourinho said. "I can not do that because I am just a manager, not a doctor".
The Old Trafford club is now through to the last four in the Europa League, where they could face either Celta Vigo, Olympique Lyon or Ajax Amsterdam.
Mourinho said he expected to find out more about the two players' injuries within "a couple of days".
Ibrahimovic, who has scored 28 goals this season, looked in huge pain after landing awkwardly in the dying embers of normal time, while Rojo also sustained a knee problem in the first half.
"He can not play every game", Mourinho said after being asked if Rashford was capable of filling in for Ibrahimovic.
"You speak about his qualities and they are fantastic".
Rooney has played just twice in 2 1/2 months due to injury niggles - the latest being an ankle problem - and the fact he has dropped down the pecking order of strikers at United, behind Zlatan Ibrahimovic and Marcus Rashford. "I always have a lot of respect for people that travels to support their team, and I think it's a lovely way for Anderlecht to be out of the competition, with honour and fight until the end, and I wish them the best for the Belgian league".
"We keep trying", Mourinho said.
United switch their focus back to the Premier League as they travel to Burnley on Sunday before travelling to Manchester City on April 27.
Mourinho also reiterated that United will battle for Champions League on both fronts - the Premier League and the Europa League.
However, there was better news later in the night as Goal reports that Luke Shaw revealed how Ibrahimovic was on his feet after the game walking around the dressing room, thus suggesting that the injury may not be as bad as first feared. "So instead of mid-May, it could be the beginning of May, this kind of acceleration of the process". "But we are in the draw for tomorrow and we still have the dream to win the competition". We got the goal in the end and everyone is happy.