Bayern captain Van Bommel extends stay
Hoeness also said defender Martin Demichelis had agreed to extend his deal until 2012.
"We have agreed with Mark to extend his contract by one year," Hoeness said on the club website after months of uncertainty.
Van Bommel, whose current deal expires on June 30, had initially wanted at least a two-year deal.
"We have agreed and I am staying," the 31-year-old, a favourite with Bayern fans, told the website.
The Dutch international had been concerned about holding on to his starting spot after Bayern agreed to sign midfielder Anatoly Tymoschuk from Zenit St Petersburg for next season.
Van Bommel joined Bayern from Spanish club Barcelona in 2006 and immediately established himself as a commanding figure in Bayern's midfield.
Bayern also agreed on a two-year contract extension for defender Demichelis, who has been with the club since 2003.
"I'm happy with the deal and I want to win a lot more with the club," the Argentina international said.