Deborah Santana cited irreconcilable differences in her Oct. 19 filing in Marin County Superior Court, the California paper said on its Web site on Thursday.
It quoted the musician's publicist as saying the pending divorce was "a private matter and there is no comment."
The couple has three children. In a 2000 Rolling Stone magazine cover story, Carlos Santana said his wife was his spiritual, emotional and financial "guiding light," adding that he would "probably be a hobo" if she had not restructured his business life in 1994.
He described himself as the "space cadet" in the relationship, and she said she had "trained" him to involve himself fully in their children's lives, take out the trash and drive the car pool when he was not touring.