The extension is a three-year, $30.75 million deal, a source confirmed.
Stewart, who was picked in the fourth round of the 2017 draft out of Albany State (Georgia), was scheduled to be an unrestricted free agent this offseason.
Stewart has seen his playing time increase in each of the past two seasons. He started 13 games last season and has started all 10 games this season.
Stewart, who lines up alongside of DeForest Buckner on the interior part of the defensive line, has 36 tackles for the NFL's second-ranked defense.
One of the keys to Stewart's success this season has been his continued weight loss. He's gone from entering the NFL at nearly 350 pounds to getting down to around 310 pounds.
"I felt that if I lost weight that I could move quicker and still have my strength,'' Stewart said. "I always want to move like a little guy ... always consider myself small, so losing weight was a big thing for me. I gained muscle and dropped a lot of fat, so I really helped myself out in the long run.''