The 36-year-old right-handed reliever is reunited with Ryan Zimmerman and Jamey Carroll.
The veteran catcher was with the Nationals in spring training last year.
The Nationals add two new managers to their minor league system and promote several coaches from within.
The Nationals will use Syracuse as their Class AAA affiliate for, at least, another five years.
The right-handed reliever split time between the Padres and Angels minor leagues last season.