The club did not announce terms of the deal but Ginobili reportedly was re-signed to a two-year deal worth $5 million.
Ginobili will join Tim Duncan and Tony Parker as the third player in San Antonio history to play at least 16 seasons with the same team. The others are Kobe Bryant, Dirk Nowitzki, John Stockton, Reggie Miller and John Havlicek.
The 40-year-old appeared in 69 games last season and averaged 7.5 points. He also shot 39 percent from the floor in 18.7 minutes per game.
Since making his debut for the Spurs in 2002, Ginobili has averages of 13.6 points, 3.9 assists and 3.6 rebounds in 992 games.
The native of Argentina also is San Antonio's all-time leader in three-pointers (1,431), ranks second in steals (1,349) and third in games played.
He is a two-time All-Star and also won the league's Sixth Man of the Year award in 2008.
In 213 postseason games, Ginobili has averaged 14.1 points. Ginobili and LeBron James are the only two players in NBA postseason history with at least 3,000 points and 300 3-pointers.