European football’s governing body had opened disciplinary proceedings the day after the game which was held up by toilet paper thrown on the pitch and a fan who ran onto the playing surface.
Arsenal have been fined €5,000 ($5,400) for a “field invasion” during the match, while Bayern must pay €3,000 ($3,240) for the throwing of objects by their fans.
“The charges against Arsenal FC were related to the field invasions by supporters,” UEFA said in a statement.
“The charges against FC Bayern Munich were related to the throwing of objects.”
Before the last-16 game at the Emirates, in which the English side were thrashed 5-1 to lose 10-2 on aggregate, fans of the German giants held up a banner reading, “Without fans football is not worth a penny,” in protest at the cost of ticket prices.
In the early stages of the game they threw a toilet roll onto the pitch causing the game to be briefly delayed.
Towards the end, there was another hold-up when a supporter evaded stewards to run onto the playing area.
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