Chamberlain, 27, will earn $1.875 million, representing a $200,000 raise from last season. The contract contains performance bonuses for games finished.
The right-hander missed the first four months of the 2012 season due to injury, going 1-0 with a 4.35 ERA and 22 strikeouts in 22 appearances. This was Chamberlain's third year of arbitration eligibility.
New York has two arbitration-eligible players remaining: righty David Robertson and lefty Boone Logan.
The Yankees have not been to arbitration since 2008, when they won their case against right-hander Chien-Ming Wang.