New York's Marcus Thames took issue with a called third strike thrown by Red Sox starter Jon Lester and argued with McClelland before Girardi rushed out to save his player, pushing Thames back to the visitors' dugout.
Girardi then continued an animated argument with McClelland, who tossed Girardi, marking the first time any Yankee has been ejected this season.
Girardi said that he was not surprised McClelland thumbed him.
"Not really," Girardi said. "I'm protecting my player, and that's all I really want to say about it."
It was Girardi's 12th career ejection and his ninth as a manager. Girardi has been tossed seven times since being hired as the Yankees' skipper before the 2008 season.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.