The deal announced Wednesday calls for a $250,000 signing bonus and salaries of $4.25 million next season and $5 million in 2015. The Rays have a $5 million option for 2016 with a $1 million buyout.
DeJesus had been scheduled to make $6.5 million next year under the 2014 option exercised by the team Sunday.
A .279 career hitter, DeJesus was acquired from Washington in a trade on Aug. 23 and started 26 games for the Rays, helping Tampa Bay earn its fourth playoff berth in six seasons.
He batted .251 with eight homers and 38 RBIs in 122 games with the Rays, Nationals and Chicago Cubs last season. DeJesus turns 34 next month.
The agreement was negotiated by agents Sam and Seth Levinson.