The Germany international's two goals were matched by Claudio Pizarro as die Roten sauntered to a comfortable win which sees them equal the league record points tally
The newly-crowned champions never looked like being beat following an own goal by Lars Stindl in the opening stages. Franck Ribery and Claudio Pizarro scored either side of a Mario Gomez double before Andre Hoffman bagged a late consolation. The visitors were not to be outdone though, and restored their five goal cushion through Pizarro in the closing stages.
Despite a few rotations in the starting line-up die Roten almost stormed into an early lead. Gomez's cross was flicked to Ribery in the fifth minute. The Frenchman's effort from the pack post looked to be destined for the top corner but his perfectly-executed attempt crashed back off the bar.
Bayern continued to get in behind the Hannover defence yet both Gomez and Thomas Muller saw the final ball narrowly evade them inside the penalty area.
However, they did not have to wait much longer for the opener. Luiz Gustavo's scything through-ball sent David Alaba down to the byeline and his cutback found its way into the net following an unfortunate deflection off of Stindl.
Five minutes later the frame of the goal denied the visitors once more as a wonderful passing move ended with a high ball over to Pizarro. The Peruvian struck it first time, but his exquisite attempt bounced down off the bar and just the wrong side of the line.
Heynckes side were utterly rampant and their second of the afternoon soon came. A stray pass from Johan Djourou was intercepted by Pizarro and he fed Ribery out to his left. The winger set himself with one touch before guiding the ball underneath Ron-Robert Zieler and into the goal.
With one eye on their Champions League semi-final with Barcelona in midweek Bayern slowed the tempo of the game, but after Stindl came close to atoning for his earlier error with a curling effort Bayern retaliated. Pizarro was again the architect, threading a pass through the channel which Gomez duly dispatched.
Zieler denied Ribery the Bavarians' fourth before half time and he was rested for the second half along with Thomas Muller as Heynckes introduced Arjen Robben and Xherdan Shaqiri.
Yet it was a Hannover substitute who worked the opposing goalkeeper first as Neuer was forced low to his right in order to stop Didier Ya Konan from having an instant impact.
Bayern were happy to coast through the game and allow Mirko Slomka's men more time on the ball, though they remained razor-sharp in attack.
With 63 minutes played Gomez put a swift in to the hosts' best spell of the game as he swept home following Jerome Boateng's cutback to the near post.
Hannover were powerless to resist Bayern and nine minutes later they found themselves five behind. Pizarro capped a fantastic afternoon as he beat Zieler to Alaba's ball at the near post and diverted the ball in from close range.
Hoffman got a late consolation for the hosts when he headed in after Neuer failed to hold Christian Pander's free kick but Pizarro restored the five-goal cushion, rounding Zieler and slotting into an empty net.
Heynckes side saw out the remainder of the game with a high level of comfort and now only need one point at home to Freiburg next week to break the Bundesliga record points tally of 81.