The deal means the sides avoid arbitration.
Nava batted .270 with 21 doubles, four homers and 37 RBIs in 113 games last season. He also played 24 games at Triple-A Pawtucket.
Nava made $556,000 last season. He had asked for a raise to $2.25 million and the team countered with an offer of $1.3 million.
Left-hander Wade Miley is Boston's last remaining arbitration-eligible player.