The star of That '70s Show, a TV series, faces up to 30 years in prison. He was led from court in handcuffs.
Three women, all former members of the Church of Scientology, accused the actor of sexual assault at his Hollywood home from 2001-03.
Prosecutors argued Masterson had relied on his status as a prominent Scientologist to avoid accountability.
The jury of seven women and five men was unable to reach a verdict on a third count after a week of deliberations, ending up deadlocked at 8-4.
