It had gone to extra-time thanks to Sofiane Hanni's effort around the half-hour mark for the impressive visitors, which cancelled out Henrikh Mkhitaryan's 10th-minute opener.
"We have Daley Blind, who has experience in the position, and I think it is time for Jones and Smalling to be courageous - to risk", the United boss, who seemed to criticise Smalling's pain threshold earlier in the season, said.
Manchester United are a step closer to the Europa League final after beating Anderlecht 2-1 in extra-time at Old Trafford.
But victory came at a cost as increasingly important defender Rojo left the field on a stretcher in the first half, before top scorer Ibrahimovic's knee buckled after landing awkwardly just before extra-time.More news: Rallies held for Pacers ahead of Game 3
Mourinho is now without two other central defenders, Chris Smalling and Phil Jones, and he urged them to make a special effort to return quickly from injury.
"He said if you need to make a change in another position I am ready for it".
"You can not do miracles, so miracles I don't expect, but they have to try to do everything to accelerate the process".
The talismanic Swede, 35, had to go off after damaging his right knee late in the game at Old Trafford and may not play again this season, while United also lost centre-back Marcos Rojo. "So instead of mid-May, it could be the beginning of May, this kind of acceleration of the process".More news: 10 things to know about Westbrook's triple-double record
"You can speak about Marcus's quality and he has that and that is fantastic but he was not scoring a goal since September", he said.
"People are saying "what do we prioritise"?"
United are joined in the last four by Celta Vigo, who eliminated Mat Ryan's Genk, Ajax and Olympique Lyon. After 90 minutes, before I knew that I have to change Zlatan, I had Ashley Young ready to come on and (Luke) told me, 'I am going to play this 30 minutes with cramps.
"I'd love to see them both", he added. "It was a hard game, difficult opponents, so I'm exhausted, I imagine the players are more exhausted than me, but we are in the draw and we still have the dream to win the competition".More news: Herrera vows to keep proving his worth
Real Madrid, aiming to win Europe's premier club competition for a 12th time, beat German champions Bayern Munich 6-3 on aggregate to reach the last four.
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