The pair were spotted exchanging words during the final stages of Wednesday night’s Champions League defeat to Bayern Munich.
It led to speculation in the press, but Flamini played down the incident when he spoke to Arsenal Player on Friday.
Mesut is a winner, I'm a winner; we were both fighting because we just wanted to give everything to the team to make sure we defended properlyMathieu Flamini
“When you're a journalist or you're a fan seeing it from the outside, it's difficult to interpret it,” he said. “But Mesut is one of my closest team-mates and we were on the pitch.
“It was not about arguing it was just about communication. Mesut is a winner, I'm a winner; we were both fighting because we just wanted to give everything to the team to make sure we defended properly.
“It was about communication, but at the end of the day it proves to everyone that we really wanted to win and we're winners. It's important, as you want a team with character, not a team who doesn't react.”
Flamini also defended Ozil's performance against Bayern.
“He is one of the players who ran the most [in that game],” he said. “He's a very offensive player and he's not used to doing so much dirty work but he did it and I'm very proud of him because he gave everything until the last minute.
“Everyone is behind him and, like I said before, he's one of my closest team-mates. We do everything together here and I feel close to him. On the pitch and outside the pitch.
“Everyone is very happy to have him here because he's such a talented player and I don't understand why people are hard on him.”Copyright 2016 The Arsenal Football Club plc. Permission to use quotations from this article is granted subject to appropriate credit being given to www.arsenal.com as the source