Ginobili, who turns 39 this month, had already said on Twitter he would be returning to the Spurs.
The Spurs were reportedly willing to go over their salary cap for Ginobili, who had sacrificed millions to help the team with cap space before.
"The San Antonio Spurs today announced that they have re-signed guard Manu Ginobili. Per club policy, terms of the contract were not announced," the team said in a statement.
San Antonio reached their cap limit this week with the signings of Pau Gasol and Davis Bertans.
Ginobili's deal is worth $14m, according to The Vertical, as he returns for a 15th season with the Spurs.