The third baseman will get a $1 million buyout and becomes a free agent after just one season with the Red Sox.
The 31-year-old Beltre led the team with a .321 batting average and a career-high 49 doubles in 154 games. He hit 28 homers and tied David Ortiz for the team lead with 102 RBIs. The option increased from $5 million to $10 million in his last game because he passed the 640 plate appearances.
Boston signed him as a free agent after he hit .265 with eight homers and 44 RBIs with Seattle in 2009.
The Red Sox must decide by Thursday whether to exercise Ortiz's $12.5 million club option.