The fit-again Dutchman scored within two minutes of entering the fray as a substitute, while Mario Gotze, Franck Ribery, Dante and Mario Mandzukic were also on target
The match was Bayern's first at the Allianz Arena in more than seven weeks, but the European champion, which won all 17 of its home league matches in 2013, showed little had changed since the turn of the year.
Mario Gotze set the home team on its way as early as the 12th minute with an exquisite finish and Franck Ribery doubled his side's advantage on the verge of halftime.
Arjen Robben, Dante and Mario Mandzukic completed the rout with second-half goals as Bayern made it 11 league wins in a row, extending its Bundesliga unbeaten streak to 44 matches in the process.
Ribery and Mandzukic returned for Bayern, while Frankfurt coach Armin Veh controversially rested defender Carlos Zambrano and midfielder Sebastian Rode ahead of a month that sees the club play eight matches in three different competitions.
Bayern quickly found its rhythm as Mandzukic's powerful effort forced a good save from Frankfurt's Kevin Trapp in the eighth minute, and Xherdan Shaqiri hit the outside of the post just two minutes later after a knock-down from the Croatian centre-forward.
Gotze was next to benefit from a Mandzukic lay-off as Dante's long diagonal ball was played into the path of the midfielder, who arrowed a finish across Trapp and into the bottom-left corner from 15 yards.
Trapp made a point-blank save to deny Gotze a second in the 23rd minute and, in a rare chance at the other end, Bayern goalkeeper Manuel Neuer reacted sensationally to keep out a deflected shot from Tranquillo Barnetta that looked to be looping in.
Ribery doubled Bayern's lead when he pounced on a loose ball inside the penalty area – after Mandzukic headed a cross against Alexander Madlung – and hooked home.
Gotze was denied by the post in the 52nd minute after his shot hit the legs of Trapp and Ribery saw a chip agonisingly hit the bar with the busy goalkeeper beaten.
Frankfurt's Joselu was sent through on goal in the 64th minute but panicked and was eventually closed down by Dante.
Robben, on the pitch for just two minutes before scoring, made Frankfurt pay almost immediately when he thrashed an effort in off the underside of the bar.
Dante then nodded in a corner for Bayern's 50th league goal of the season in the 69th minute and Mandzukic capped the performance with a minute to play, curling past Trapp with his left foot after beating Marco Russ.