The Germany Under-21 international will move to the Allianz Arena at the end of the season, having been with Frankfurt since 2010.
Rode has been a regular for Frankfurt in Germany's first and second tiers since joining from Kickers Offenbach and will move to Bayern on a four-year contract.
"I am very pleased that this transfer has worked out," Rode told Bayern's official website.
"FC Bayern is the next big step for me. I want to develop myself here and win a lot of titles with my future team-mates."
Rode has played 17 times in the Bundesliga this season, helping Frankfurt to a comfortable mid-table position of 11th, and Bayern's sporting director Matthias Sammer backed the 23-year-old to adapt to life with the European champions.
"Sebastian Rode is an excellent professional, he embodies the highest level of professionalism and dynamism," Sammer stated.
"I am sure that he will give our team a lot of momentum and enthusiasm to handle future tasks."
