The surgery was performed by foot and ankle specialist Dr. Mark Berkowitz at the Cleveland Clinic.
Naylor and rookie second baseman Ernie Clement ran into each other as they converged on a fly ball in short right field. Naylor's foot got trapped underneath him after he slammed into Clement. Naylor was sent sprawling and his lower right leg was bent back awkwardly.
Naylor is batting .253 with seven homers and 21 RBIs while playing right field and first base. The 24-year-old was acquired from San Diego last season.
The Indians' injuries continue to mount. Third baseman Jose Ramirez was scratched shortly before Friday's game against Houston because of a sore left elbow. The team said he was injured diving for a ball Thursday. Ramirez also missed a game Wednesday after fouling a ball off his left cheek.
Eddie Rosario was out after leaving Thursday's game with right abdominal tightness. Manager Terry Francona said the left fielder's MRI came back clear.
Designated hitter Franmil Reyes was activated Friday after being out since May 23 with a strained oblique. He was in the lineup and batting fourth.
Catcher Roberto Perez, who had finger surgery May 7, is expected to be activated Saturday.
Infielder Yu Chang was optioned to Triple-A Columbus to make room for Reyes.