Two quick goals from Bastian Schweinsteiger and Mario Mandzukic effectively ended Schalke's hopes midway through the first half before Franck Ribery and Claudio Pizarro finished the Royal Blues off.
Meanwhile, Bayern goalkeeper Manuel Neuer maintained his record of never having conceded against his former club.
Bayern had to survive an early wave of Schalke pressure before getting a foothold in and, eventually, control of the game.
Kevin-Prince Boateng sent in the first shot which Neuer just managed to push away to his right.
A quick break down the right from Jefferson Farfan enabled the Peruvian to send in a cross in the 17th minute which Adam Szalai met at full stretch, although he could only lift the ball vertically in front of the goal rather than on target.
Bayern's first attack resulted in the opening goal in the 21st minute with Arjen Robben's corner headed in by the unmarked Schweinsteiger as Atsuto Uchida made a weak attempt to clear the ball off the line.
Less than 60 seconds later, it was two with Ribery sending David Alaba clear down the left and his cross was headed in by Mandzukic with Benedikt Howedes only helping the ball across the line rather than clearing.
Given that Neuer had never conceded against his former club, Bayern's win was already reasonably safe.
Arjen Robben shot wide after exchanging passes with Schweinsteiger before half-time and, although Julian Draxler and Boateng both flashed shots wide, a Schalke recovery was not forthcoming.
Instead, Bayern increased their lead in the 75th minute with Alaba getting in around the back and pulling the ball back for Ribery, who did not make the best of contacts, but still managed to bundle the ball over the line.
Substitute Pizarro then added a fourth which had more than just cosmetic significance.
Dante's long ball forward sent Thomas Muller clear and he drew Timo Hildebrand towards him before squaring for the Peruvian to score into the unguarded net from 10 yards, allowing Bayern not only to join Dortmund, but to equal the goal difference of the Westphalians.