Despite playing without the injured Arjen Robben, the besieged Franck Ribery and a resting Mark Van Bommel, Bayern were still too strong and triumphed with late goals from German World Cup stars Thomas Müller and Mirsolav Klose.
They dominated the match with Bastian Schweinsteiger missing a good eighth-minute chance while Klose saw a 51st-minute drive come off the post. But they had to be patient for the breakthrough.
Müller, who was handed a lucrative new contract on Friday which ties the 20-year-old to the club until 2015, found the target in the 75th minute.
Klose added the second six minutes later as Bayern won a third Super Cup, a trophy which hadn't been contested since 1996.
"This team is better than last year's because everyone knows what they have to do," said Bayern coach Louis van Gaal, who led the team to the Champions League final last season.
Schalke 04 coach Felix Magath, who tempted Spanish star Raul to leave Real Madrid in the summer, remains cautious over whether or not his team can chase Bayern all the way, just as they did last season when they finished runners-up.
"You must see that we haven't yet got the quality to beat a high-level team," he said.