Chamberlain was ejected with one out in the ninth inning after tossing two straight pitches directly over the head of Red Sox third baseman Kevin Youkilis.
MLB Vice President of On-Field Operations Bob Watson said Chamberlain has been fined an undisclosed amount.
"A couple balls slipped,” Chamberlain told reporters after the game. "We're trying to win ballgames. I have nothing but respect for him. Youkilis plays the game hard, and it was nothing against him. There's no chance I'm trying to do that."
"That's absolutely ridiculous that you have this kid who's up here trying to prove himself trying to throw the ball through the wall," said an angry Yankees Manager Joe Torre.
The suspension is scheduled to begin with Friday night's game against Tampa Bay.