The Red Devils beat their Belgian opponents 2-1 at Old Trafford, 3-2 aggregate, to progress to the last four of the competition, with 19-year-old forward Marcus Rashford scoring the victor in extra-time.
Manager Jose Mourinho offered a negative prognosis on both Ibrahimovic and defender Marcos Rojo, who also suffered a knee injury against Anderlecht, following the game.
Henrikh Mkhitaryan had given United an early lead at Old Trafford but the hosts were pegged back when Sofiane Hanni equalised to send the game into extra-time. Some players don't understand what I want, what it takes for me to trust a player, but Marcus I trust.
"Herrera plays. He didn't play (against Anderlecht)", said Mourinho.
Injuries to Zlatan Ibrahimovic and Marcos Rojo marred United's progress to the last four of the Europa League and Mourinho accepted he faces tough team selection issues for Sunday's Premier League trip to Burnley. I think that's the final nail in the coffin for him, definitely.
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Rojo was carried off in the first half on a stretcher while Ibrahimovic hobbled off late in the game after landing awkwardly following an aerial challenge.
Mourinho said. "It is hard for the kid to play every match, but I always trust the players with a special mentality". They have injuries and even in the insane mentality they can not play Sunday. The Belgian side equalised via Sofiane Hanni in the first half itself, before the two teams battled it out for the rest of regulation time in search of a victor. I watch more games of football than I eat bags of crisps.
Zlatan has scored 28 goals including the victor at Wembley in the Community Shield and the League Cup final, plus other 17 goals from 28 league appearances.
United find out their semi-final opponents in Friday's draw, with Ajax, Celta Vigo or Lyon lying in wait. We don't have Jones or Smalling.
He added: "When it is not mathematically possible to qualify (for the Champions League) through the Premier League is when we put everything into the Europa League".