Thames took the third pitch of his at-bat from Jon Lester and McClelland hesitated before giving the strike signal. Thames protested and Girardi came from the dugout to move his left fielder away. The manager then turned his attention to McClelland and was ejected for the ninth time in his career as a manager, seven of them with the Yankees.
Girardi also was ejected three times as a player, one of them with the Yankees.
Thames returned to the dugout, smacked his bat on a step and flung his helmet to the ground.
Information from The Associated Press contributed to this report.