The Spanish coach says that his side were better over the two legs despite not playing with his strongest XI for Tuesday's home game, which they drew 1-1 to progress on aggregate
The defending champions progressed into the quarter-finals of the competition after beating Arsene Wenger's side 3-1 on aggregate as Tuesday night's 1-1 draw in Munich followed the Germans' 2-0 victory at the Emirates Stadium in February.
Guardiola argued that, apart from the early exchanges in the first leg, his side were the better team in both games against the Londoners.
"They were better for eight minutes in the first leg," he told Sky Sport Germany. "For the rest of the time we were superior.
"Arsenal had no chances in the first half. They defended with many players and we controlled the match, except for the goal we conceded - and that could have been a foul.
"We had a 2-0 advantage from the first leg. We limited our mistakes and did not allow Arsenal any counterattacks. We played on a very high level and now we are in the quarter-finals."
The former Barcelona coach was asked if he fielded his best 11 players for the second leg, to which he replied: "No. [Toni] Kroos, [Thomas] Muller, Claudio [Pizarro] and Rafinha all deserved to play too. I see them in training every day and they work hard.
"But we have to think of how we can play best and how we can control best and according to that I have to decide. Tomorrow it can be completely different. It is a decision totally based on tactics."
Bayern star Arjen Robben believes that a draw was the right result on the night but that the Germans deserved to progress through to the next phase.
"They have a very good team," he told Sky Sports. "They have a lot of quality on the pitch. The main thing for us was to keep possession and control the game.
"When we scored it looked like we were in a comfortable position but then they scored. I think it was a deserved draw but also deserved that we go through to the quarter-finals."