Marco Borriello pulled one back for the hosts at the start of the second period, finding the net from a prone position after slipping as he went to meet Jeremy Menez's cross following a rampaging run.
Daniele De Rossi restored parity nine minutes from time and it was left to Roma legend Francesco Totti to hit the winner from the penalty spot six minutes from time, with Bayern confirmed as group winners despite the defeat.
Basel are still in with a chance of stealing second spot following their narrow success at home against CFR Cluj.
Federico Almerares gave the Swiss side the lead with 15 minutes on the clock as he slid in to fire home at the far post, with Felice Piccolo dismissed for the visitors late on.
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