But Arsenal should have gone ahead themselves six minutes later when Pierre-Emerick Aubameyang's lightning run led a counter-attack, he played in Mesut Ozil whose shot was blocked by Manuel Neuer.
But an 88th-minute victor from 20-year-old substitute Nketiah handed Unai Emery's side the win in Los Angeles.
The Gunners went 1-0 up after a 49th-minute own goal from Bayern defender Louis Poznanski on Wednesday. "If you really want to make a dent in the Champions League, then we could perhaps still use one or two".
Unai Emery will be keen to add another victory under his belt following his side's serene win over Colorado Rapids yesterday, with youngsters Bukayo Saka, James Olayinka and new signing Gabriel Martinelli all finding the back of the net.