The "Working Girl" star filed for the split from the Spanish actor in Los Angeles County Superior Court on Friday, citing irreconcilable differences, according to the Associated Press and TMZ, which obtained the documents.
The actress petitioned for spousal support, child support and sole physical and joint legal custody for their daughter Stella, who turns 18 in September.
She is willing to pay her own legal fees and the couple is expected to divide up their property, which includes real estate in the U.S. and Spain, TMZ said.
The "Hawaii 5-0" guest star signed the petition on May 30 but did not list a date of separation.
Griffith, 56, and Banderas, 53, sparked their romance on the set of their 1995 film "Two Much." In 1999, Banderas helmed the film "Crazy in Alabama," which starred his wife.
Griffith also has a tattoo of "The Mask of Zorro" star's name in a heart on her right shoulder, AP said. However, they've dealt with a spate of breakup rumors much of this year, the Daily Mail reported.
It's the second divorce for Banderas, who was previously married to Spanish actress Ana Leza for nine years, but they split in 1996.
The Golden Globe-winning actress, who is the daughter of former model and actress Tippi Hedren and ad exec Peter Griffith, already has three other divorces under her belt.
The "Lolita" star was previously married to Steve Bauer and twice to actor Don Johnson and they have a daughter together, Dakota Johnson, the star of the upcoming "50 Shades of Grey" film adaptation.
Griffith was spotted wearing her wedding ring on the star-studded red carpet for the AFI tribute to Jane Fonda on Thursday at the Dolby Theatre in Hollywood. The actress posed with "Desperate Housewives" star Eva Longoria and "The Mask of Zorro" star Catherine Zeta-Jones, among other famous faces.