Ortiz, who has 32 home runs and 99 RBIs, is sidelined because of a bruised right foot that has been bothering him since he fouled a pitch of it on Aug. 24.
Napoli, second on the Red Sox with 17 home runs, had a dislocated left ring finger and a sore toe.
Allen Craig replaced Napoli at first base and batted fifth. Craig has hit .100 with one homer and two RBIs in 50 at-bats since he was acquired from St. Louis on July 31.
Outfielder Daniel Nava was the designated hitter and batted third.