The veteran shortstop left in the eighth inning and was sent for X-rays, which came back negative, but it's not immediately clear when he'll be able to return to the lineup.
"Yunel came out after getting hit the second time," manager John Farrell said. "X-rays were negative and still day to day for him."
Escobar was hit twice in the game by fastballs from Nova. The first incident occurred in the fourth inning when Escobar was struck in his left shoulder, but the second situation proved to be more troublesome.
Nova worked the count to 1-1 before his 93-mph fastball struck Escobar on the left elbow. Both dugouts were immediately warned by home-plate umpire Jim Joyce, and Escobar was slow getting to first base as he glared back at the mound.
Escobar remained in the game, but he was pulled for pinch-hitter Omar Vizquel. He becomes the second player this series to leave with an injury, as Colby Rasmus was forced to depart Friday night's game after the eighth inning with a strained right groin.