Pep Guardiola's men dominated huge periods of the game against Wolfsburg but his Bayern side were forced to be patient before eventually finding the net through Coman.
Leverkusen coach Roger Schmidt refused to be sent to the stands after he was sent off for protesting Pierre-Emerick Aubameyang's second-half winner over Leverkusen.
The Bavarians dropped points in the Bundesliga for the first time in four matches as they were held to a stalemate against Leverkusen after a disciplined display from the hosts.
The Bundesliga champions secured a place in the next round of the competition, despite an unconvincing performance.
Pep Guardiola's side went behind at Allianz Arena but fought back in the second half with two goals from the Germany international and a Robert Lewandowski strike sealing the win.
The Poland international once more demonstrated his class in front of goal to keep the Bavarians eight points clear at the top of the Bundesliga.
A terrific strike from the Armenia international has allowed BVB to keep the pressure on Bayern at the summit of the German top flight.
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