The former Germany Under-21 international joined the club from FC Koln in 2012 and has since played 41 league games scoring six goals.
The club did not disclose the length of the contract.
Freis has made 20 league appearances this season, scoring twice as Christian Streich's men sit a point from safety and sporting director Jochen Saier believes the 28-year-old's experience could prove vital.
"Sebastian Freis is one of our more experienced players, which is important for the young team with his play, his attitude and his character as a team player," he told www.scfreiburg.com.
"He embodies an important building block in our squad planning for the coming season."
Freis added: "They were good conversations in which I came to the conclusion that I would definitely stay at SC Freiburg.
"I identify myself fully with the concept of the club, so I am glad that we go on together."