The team announced the move Saturday. The sides agreed to the deal on Dec. 18, pending a physical.
In his first season as the Detroit Tigers' closer, Benoit had 24 saves in 26 chances this year. But in Game 2 of the AL Championship Series, he allowed a tying grand slam by Boston's David Ortiz that was a turning point in the series.
To make room for Benoit on the 40-man roster, the Padres designated minor league right-hander Adys Portillo for assignment.