The club picked up the 2013 option for their closer, who posted 32 saves and a 2.82 ERA in 57 appearances this year.
"J.J. has done a tremendous job for us over the past two seasons and is the leader of our bullpen," Diamondbacks General Manager Kevin Towers said in a written statement. "We are looking forward to bringing him back in the same role next season."
Putz, 35, is 33-31 lifetime with 183 career saves and a 3.04 ERA in 10 seasons with four Major League teams.
He was 1-5 last season but converted 19 straight save opportunities and tied a team record with 24 consecutive scoreless innings.