The council, acting as the stadium authority board, voted 7-0 in favor of the deal, in which the jeans maker will pay $220 million over 20 years to have the facility named Levi's Stadium.
"It's a testament to why we always thought this project would work," 49ers CEO Jed York said after the meeting, the Mercury News reported. "To anybody who ever doubted this project would happen, these numbers speak for themselves."
The $1.2 billion stadium in Santa Clara is scheduled to open for the 2014 season.
The state-of-the-art venue is considered the favorite to host Super Bowl L in 2016.