The filing comes nearly two years after they announced their separation.
The petition cites irreconcilable differences as the reason for the split. The filing says neither person should get financial support and that the two have agreed on how to split their assets. The documents say they should have joint custody of their 16-year-old daughter and 15-year-old son.
The two met and started dating in 2005, but did not legally marry until 2017. It will be at least six months before a judge declares them divorced.
It was the first marriage for Momoa and the second for Bonet, who was previously married to musician Lenny Kravitz and has another daughter, actor Zoe Kravitz, with him.