Ibrahimovic, 35, landed awkwardly when challenging for the ball, while Rojo, 27, was replaced on 23 minutes after colliding with a visiting player.
Mourinho told BT Sport after the 2-1 win at Old Trafford: "I don't think they are easy injuries, but I prefer to wait for all the tests to be done tomorrow.
"I want to wait. My feeling is not great for both. I want to be optimistic, but I'm not. I can't say any more than that, I am not a doctor. But the news is fairly negative I think."
Man United will learn their semi-final opponent in Friday's Europa League draw at noon BST, with Celta Vigo, Lyon and Ajax joining the Premier League outfit in the pot.