Griffith, 56, and Banderas, 53, married in 1996 after striking up a romance filming the comedy "Two Much" and have a 17-year-old daughter, Stella Banderas.
"We have thoughtfully and consensually decided to finalize our almost 20 years marriage in a loving and friendly manner honoring and respecting each other, our family and friends and the beautiful time we have spent together," Griffith and Banderas said in a statement issued by their publicist.
Griffith requested physical custody of Stella, who turns 18 in September, but joint legal custody, with the "Desperado" star allowed visitation.
The actress, who earned an Oscar nomination for her role in the 1988 romantic comedy "Working Girl," also requested spousal support from Banderas.
This was the fourth marriage for Griffith and the second for Banderas. Griffith was married to actor Don Johnson twice and also Steven Bauer. Banderas was married to Spanish actress Ana Leza.