Although Juve needed only a draw from the final Group A game to join leaders Bordeaux in the knockout stages, Bayern were the brighter side from the start and routed their opponents.
David Trezeguet converted Claudio Marchisio's cross on 19 minutes to give the hosts the lead against the run of play.
However, the Germans levelled on the half hour when defender Martin Caceres needlessly fouled Ivica Olic and keeper Butt surprisingly popped up to score the penalty.
Striker Olic then put Bayern ahead seven minutes into the second half after Gianluigi Buffon, carrying a knee injury which will now need surgery, could only parry Daniel van Buyten's effort.
Mario Gomez netted following a corner in the 83rd minute and substitute Anatoliy Tymoshchuk slammed home in injury time to embarrass the Serie A side, who had drawn 0-0 in Munich.
FALTERED THROUGH
Bayern's qualification for February and March's first knockout stage is an impressive achievement after they faltered through their opening games both in Europe and the Bundesliga.
Coach Louis van Gaal was under pressure until three wins in a row heading into the must win clash in Turin, where Bayern could easily have scored more with Ivic hitting the post among other chances.
Juventus's counterpart Ciro Ferrara, in his first full season as a manager, has presided over an unconvincing spell of results but Saturday's 2-1 win over Serie A leaders Inter Milan had appeared to give his side a boost in confidence.
His job could now be under threat despite clinching of a Europea League berth after Juve never looked like getting the point they needed, even after going ahead.
Big close season signings Diego and Felipe Melo were again poor and were heartily booed by the Stadio Olimpico.
