Pomeranz appeared to tweak something, and manager John Farrell decided to remove him from the game after he attempted two warm-up pitches.
Prior to leaving, Pomeranz had allowed four hits and no runs while striking out four in 3.1 innings with Boston leading 2-0.
Pomeranz was replaced in the game by long reliever Brandon Workman.
Boston has dealt with injuries to key starters all season long with David Price and Steven Wright currently on the disabled list, and Eduardo Rodriguez having previously spent time on the DL as well.
Pomeranz has been a constant for the Sox, though, boasting a 12-4 record with a 3.31 ERA, 1.34 WHIP and 136 strikeouts in 130.2 innings.
He made his first career All-Star team with the San Diego Padres last season before San Diego traded him to Boston for highly touted prospect Anderson Espinoza.
The 28-year-old Pomeranz is key for the Red Sox down the stretch and heading toward the playoffs, but Boston entered Friday with a cushion of four games over the Yanks in the AL East.