Dutchman Van Bommel, who joined Bayern in 2006 from Barcelona, has been instrumental in the team's run to the Champions League quarter-finals and their return to the top of the Bundesliga standings this season.
Bayern are also in the German Cup semi-finals.
"It was my wish to extend it by a year," the 32-year-old defensive midfielder said in a statement.
He almost left the club at the end of last season after Bayern refused to give him a two-year contract extension opting to offer a one-year deal, which he grudgingly accepted.
"I want to be successful with the team and win titles. This is our goal for this year and the next," van Bommel said.
He joined Bayern fresh from his Champions League win with Barca and quickly established himself as the leader in midfield, renowned for his tough defending and short temper as well as his scoring abilities.
Bayern general director Karl-Heinz Rummenigge said: "In the past years, but especially in the past months, Mark has been a good, important and stable guarantor of success.
"We are very happy to have agreed to an extension before these tough weeks that lie ahead."
