Bayern took an early 10th minute lead when Lewandowski made the most of some poor Arsenal defending but Özil put the ball in the back of the net just minutes later only to have the goal ruled out for a handball.
The controversial decision did not go down well with Özil who started swearing at the referee in his mother tongue.
Özil swore at the referee in Turkish telling the referee to f off which in hindsight was a pretty smart way to vent his frustration as he had already been booked for handling the ball.
Bayern Munich v Arsenal
Kick-Off: 19:45 GMT
Referee: Gianluca Rocchi
Stadium: Football Arena Munchen
Bayern: Neuer; Lahm, Martínez, Boateng, Alaba; Alonso; Robben, Thiago, Douglas Costa; Müller, Lewandowski.
Out: Götze (groin), Ribéry (ankle), Rode (thigh)
Doubtful: Badstuber (thigh), Bernat (groin)
Arsenal: Čech; Debuchy, Mertesacker, Gabriel, Monreal; Coquelin, Cazorla; Campbell, Özil, Sánchez; Giroud.
Out: Walcott (calf), Oxlade-Chamberlain (hamstring), Arteta (ankle), Ramsey (hamstring), Ospina (shoulder), Wilshere (calf), Rosický (knee), Welbeck (knee), Bellerín (groin)
Goals: 10′ Lewandowski, 29′ Muller, 42′ Alaba, 55′ Robben, 69′ Giroud, 89′ Muller