First-year manager David Ross had Willson Contreras and Victor Caratini in his starting lineup for Game 1 on Wednesday, so the addition of Phegley gives him a third catcher in case of injury. Left-hander Josh Osich was designated for assignment to make room for Phegley on the 40-man roster.
Vargas, who was claimed off waivers from Minnesota on Sept. 5, was activated from the 10-day injured list after missing the last part of the season with a right hamstring strain.
The Marlins had infielder Lewin Diaz, left-hander Braxton Garrett and right-hander Nick Neidert on their roster for their first playoff appearance since they won the World Series in 2003. Pitchers Jose Urena, Nick Vincent and Dan Castrano were transferred to the team's taxi squad.
Urena broke his right forearm when he was hit by a line drive Sunday against the New York Yankees.