The first leg ended 1-1 at Old Trafford after Simon Kjaer cancelled out Amad Diallo’s goal in the closing moments of the game.
Ibrahimovic came on in the second half but he was unable to make any difference in the match as Manchester United held on to victory.
Tottenham crashed out in alarming fashion losing 3-0 after extra time to Dinamo Zagreb.
The Mourinho led side win the first leg 2-0 and it was expected that they will complete the job in Croatia.
Mislav Orsic scored a sublime hat-trick to lead Dinamo Zagreb to a shock victory and a place in the Europa League last eight.
Arsenal lost 1-0 to Olympiakos at the Emirates Stadium but it wasn’t enough to deny them a place in the quarter-finals after winning the first leg 3-1 in Greece.
Glasgow Rangers lost 2-0 at home to Slavia Prague to crash out after a 1-1 draw in the first leg.
Ajax defeated Young Boys 2-0, while Villarreal earned a 2-0 victory over Dynamo Kiev.