Both players are in the lineup Sunday against Colorado.
Bonifacio was on the DL for the second time because of an injured left thumb. He had surgery May 18 to repair a ligament and missed 46 games. He aggravated the injury on Aug. 3 and missed another 14 games.
Bonifacio is hitting .261 with 30 stolen bases in 61 games.
Murphy strained his left hamstring Aug. 3 and missed 14 games. He is hitting .194 in 33 games with the Marlins.
To make room for Bonifacio and Murphy on the roster the Marlins optioned outfielder Scott Cousins to Triple-A New Orleans and designated infielder Gil Velazquez for assignment Saturday night.