Nixon, along with teammate Gabe Kapler, were among 24 players to file on the second day of free agency, bringing to 83 the total number to put themselves on the open market.
The seventh overall pick in the first round of the 1993 First-Year Player Draft was the last connection to former general manager Lou Gorman and is the longest-tenured member of the Red Sox organization.
Nixon, 31, struggled to stay on the field over the last several years, injuring his back and quadriceps in the club's World Series run in 2004. This season, he was hitting over .300 before injuring his right elbow July 30, finishing the season with a .268 average, eight homers and 52 RBI.
Still, the right fielder with the perpetually soiled cap has 133 homers in a Red Sox uniform, good for 16th on the club's all-time list.
Kapler, who like Nixon is 31, batted .254 with two homers and 12 RBIs in 2006 after battling back from a ruptured right Achilles tendon late in the 2005 season. The reserve outfielder left Boston after the 2004 season for a brief tenure in Japan in 2005 before returning to the Red Sox midway through the '05 season. He has 64 homers and is a lifetime .270 hitter since making his big-league debut with Detroit in 1998.
With Doug Mirabelli submitting his paperwork Saturday, the Red Sox now have three players who have filed for free agency.
Saturday was the first day after the World Series, and the first day eligible players could file under Article XX B(2) of Major League Baseball's Basic Agreement.
Mike Petraglia is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.