It will be the second time the 68,500-capacity venue has staged the NFL showpiece after hosting Super Bowl 50 in 2016.
In that game, a Peyton Manning-led Denver Broncos team upset the Carolina Panthers 24-10 in what would turn out to be Manning's farewell appearance.
"The Bay Area was an incredible host for Super Bowl 50, and we are thrilled to bring the Super Bowl back," NFL Commissioner Roger Goodell said in a statement.
"We look forward to working with the 49ers and the Bay Area Host Committee to create an impactful Super Bowl LX in 2026 that showcases all the great things the region has to offer."
The 2026 announcement was taken at the NFL's spring meeting in Minneapolis.
The Super Bowl will be staged at the Allegiant Stadium in Las Vegas in 2024 before heading to New Orleans for the 2025 edition.
