Pierre-Emerick Aubameyang scored with a sensational bicycle kick and had a chance to seal the tie with the final kick of the game, but somehow fired wide from six yards out.
Ajax, Celtic, Benfica and Porto went out but Manchester United hardly broke sweat after Simon Deli of Brugge conceded a penalty and earned a red card in the 23rd minute at Old Trafford and won 5-0.
Manchester United will take on Club Brugge in the last 32 of the Europa League while struggling Arsenal will face Greek side Olympiakos.
Champions League: Jose Mourinho was quick to acknowledge the ball boy's contribution to Harry Kane's first goal against Olympiacos FC as he went up straight to him and shook hands with him.
The incident prompted the Olympiakos team to leave the pitch in protest before riots erupted outside the ground.
The Greek league match between hosts Panathinaikos and arch-rivals Olympiakos was delayed after home fans clashed with police before the game and threw flares at Olympiakos players.
Thomas Mueller, who has been in tremendous form, netted twice while Mario Goetze also struck a goal to help FC Bayern Munich beat Olympiakos 3-0 in their Champions League match.