The Bundesliga champion said on its home page on Thursday that an examination one day after the injury "confirmed the fears" and showed that Martinez had torn ligaments. Bayern said Martinez will be sidelined for "at least the rest of this year."
He will undergo surgery in the United States shortly before returning to Germany to start rehabilitation.
"Of course I am very sad at the moment. But don't worry, I will be back even stronger," the 25-year-old Spain international said in the statement.
Martinez was injured in the 31st minute of a 2-0 loss in the German Super Cup at Borussia Dortmund when he tried to take a shot and hit the hip of Dortmund's Marcel Schmelzer.
Bayern coach Pep Guardiola used a three-man defense, with Martinez in the middle. It remains to be seen whether Guardiola will continue with that formation.
Martinez needed groin surgery in September 2013.
Martinez' injury compounds Guardiola's problems ahead of the season. Six of Bayern's World Cup winners with Germany only recently rejoined the team. Wingers Arjen Robben and Franck Ribery are nursing injuries, while midfielder Thiago Alcantara and defender Rafinha won't be back for weeks, if not months.
Bayern could still test the transfer market, although team officials had said earlier that no new arrivals were in the cards.
Central defender Holger Badstuber is back but lacks match fitness after sitting out nearly a year and a half following two knee surgeries.
The first round of the German Cup is this weekend with Bayern playing third-division Preussen Muenster, before kicking off the Bundesliga season on Aug. 22 against Wolfsburg.