After 12 years of marriage, Ms. Phillips, 43, alleged "irreconcilable differences" between the couple, according to paperwork viewed by US media.
The 47-year-old Masterson was sentenced to 30 years to life in jail earlier this month while she was present in court.
They got married in Ireland in 2011 after becoming engaged in 2009.
divorce petition was submitted on Monday in Santa Barbara Superior Court and asks for spousal maintenance as well as complete custody of their child, both legally and physically
Ms. Phillips, a former adolescent model and singer-turned-actress, supported her husband during the drawn-out legal proceedings surrounding the three rape allegations that date back to 2003.
Last year, a mistrial resulted from a jury that couldn't agree on any of the charges against Masterson.