Paul Scholes, working as a pundit for BT Sport, suggested United were lucky to be awarded a 90th minute spot-kick after Yan Brice was adjudged to have caught Fernandes in the face but Solskjaer said afterwards the clash was serious enough to close up one of Fernandes' eyes before he took the penalty.
"I haven't seen it [the incident], I've just seen his eye when he came off, he got hit," said Solskjaer. "Mike Phelan was sat behind me in the dugout and said he took one in the face. His eye is red and to score with one eye open is also a skill."
United will be expected to advance to their fifth semifinal under Solskjaer when Granada visit Old Trafford next week but they will have to negotiate the second leg with a depleted squad.
"Losing three players is not a good position to be in," said Solskjaer. "I don't think we deserved five yellow cards but that's happened. We're delighted with the result of course."
Rashford will be assessed on their return to Manchester after coming off in the second half against Granada as he continues to manage an ankle injury.
"It's the same thing as before, he's not recovered from it and hopefully it's not gotten any worse from this," said Solskjaer. "I think he should be ready for Sunday [vs. Tottenham Hotspur]."