The team announced the deal Wednesday that takes Kilgore through the 2020 season. Last week, Garoppolo signed a $137.5 million, five-year contract.
Niners general manager John Lynch says it was important to reach a deal with Kilgrore ahead of the free agency period.
The 30-year-old Kilgore started a career-high 17 games last season. A fifth-round draft pick in 2011, he has made 39 career starts in 74 regular-season games. He has started in each of his past 32 games.