Arsene Wenger's side were thumped 5-1 at the Allianz Arena in the first leg, before Bayern replicated that scoreline at Emirates Stadium three weeks later.
Ozil featured in both those fixtures and the Germany international – who has come under criticism himself during Arsenal's poor run of form – has opened up about the encounter.
"The devastating loss at Bayern Munich this season is undoubtedly one of the darkest hours of my footballing career," Ozil says in his book 'Gunning for Glory', which is being serialised in the Mail on Sunday.
"It's in the top five of the most humiliating defeats I've suffered.
"We were positively prepared for the game. Arsene Wenger had revealed to us his game plan. He was very clear about his ideas – and they were good ones.
"Our intention was to go all out for Bayern's central defender Mats Hummels; to prevent him from opening up the game which he does so brilliantly.
"In this way we hoped we'd be able to stop Bayern from building up the play at an early stage and disrupt their rhythm.
"Of course I could go on about why our game plan didn't work. I could look for excuses. But I'm not going to. What went on between us in the dressing room after the match is nobody's business.
"Nor is what Wenger considered our failures to be in his post-match analysis. The fact is, we all failed. We were all bad."
However, despite the humiliation, Ozil is determined that Arsenal will use it as a learning experience.
"It was a performance we can't just brush aside. No, we have to learn our lessons from it," said the 28-year-old.
"We all have to ask searching questions of ourselves and accept responsibility for the defeat. All the players, all the trainers, even the management.
"I have thought long and hard about the match. I've visualised what went wrong. But I can't allow this game to inhibit me in the future and destroy my confidence, which is the most important thing a footballer can have on the field. This defeat mustn't get the better of any of us."
Arsenal have slumped down to seventh place in the Premier League after a return of just seven points from eight matches, though could move back up to fifth should they beat Middlesbrough on Monday.