The former Germany international has held the role with the Bundesliga champions since 2012, with the club winning a host of domestic and European titles since then.
Sammer signed the new deal on Wednesday, with the 47-year-old now under contract at the Allianz Arena until June 2018.
"I am grateful for the confidence of the board but also for the good cooperation with my colleagues," he said in a statement on the club's official website.
"I promise that I will continue with the same passion and intensity with which I have fulfilled this task so far.
"We all have big goals with Bayern. I want to help us to achieve this."
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