Proctor had Tommy John surgery on Tuesday. He consulted with specialist Dr. James Andrews before the operation.
Proctor had surgery in October to repair a partially torn flexor tendon and his return was repeatedly delayed when he felt pain throwing. Last week, Proctor was shut down after about a dozen pitches in the bullpen in a side session.
"It's a loss for us and for him, too, to miss a season. I've never seen anybody work so hard to try and get through this season without having that surgery," Marlins manager Fredi Gonzalez said. "His last side was painful. He tried to let it go and he threw two pitches where he screamed, and he just couldn't do it."
Known for a heavy workload, Proctor pitched last season for the Los Angeles Dodgers. He signed with Florida in the offseason.
Proctor was moved to the 60-day disabled list. The Marlins called up lefty John Koronka from Triple-A New Orleans to start Tuesday night against Milwaukee.