Bonifacio was awarded a $2.2 million salary by a three-person panel on Wednesday rather than the Marlins' offer of $1.95 million. Arbitrators Steven Wolf, Mark Burstein and Sylvia Skratek made the decision a day after hearing arguments.
Pitcher Anibal Sanchez beat the Marlins in a case decided Monday and will make $8 million instead of the team's $6.9 million offer.
Bonifacio hit a team-high .296 last year with five homers, seven triples, 36 RBIs and 40 steals in 51 tries. The infielder-outfielder made $425,000.