Top scorer Ibrahimovic’s knee buckled as he landed following an aerial challenge in the Anderlecht box late in normal time and he went down grimacing in pain before hobbling off.
Rojo succumbed to a knee injury in the first half at Old Trafford and had to be stretchered off, with Daley Blind taking his place.
“I don’t think they are easy injuries, but I prefer to wait until all the tests are done and then speak. I can’t do that because I am a manager not a doctor,” Mourinho told BT Sport.
“But the news is fairly negative I think.”
After receiving treatment from United’s medical staff, Ibrahimovic was able to limp down the tunnel, with Anthony Martial coming on as a replacement.
Ibrahimovic, 35, has been a sensation since joining on a free transfer from Paris Saint-Germain last year, scoring 28 goals and inspiring United to victory in the League Cup.
Rojo’s injury deprives United of another centre-back at a time when Chris Smalling and Phil Jones are already sidelined.
“It is disappointing. Hopefully it is not too serious because they are two big players for us,” said midfielder Michael Carrick.
United prevailed 2-1 on the night, and 3-2 on aggregate, courtesy of an extra-time winner by Marcus Rashford.
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