The injury happened in the sixth inning on Thursday against the Blue Jays with Johnson attempting to bunt. Girardi said his status is day to day.
Johnson was hitting .333 during his last 10 games, which earned him back his regular spot in the lineup.
"It's not what you want," Girardi said. "It is unfortunate, but we don't think it will be long."
Yangervis Solarte started in Johnson's place at third and hit ninth in the lineup. Solarte has scuffled a bit lately after a fast start. He has not had a hit since June 8 against the Royals, although he did force in a run by drawing a bases-loaded walk on Thursday.
"It's just kind of what you go through as a hitter," Girardi said. "I haven't seen a big change in his at-bats."
Jamal Collier and Jake Kring-Schreifels are associate reporters for MLB.com.