The 27-year-old had two seasons of arbitration remaining and will still be eligible to hit free agency following the 2021 season.
Story is coming off his second straight All-Star season, hitting .294/.363/.554 with 35 homers and 23 steals while claiming his second consecutive Silver Slugger award.
Story was entering his second year of arbitration and had filed for a one-year, $11.5-million settlement, according to Mark Feinsand of MLB.com. Meanwhile, the Rockies countered with a $10.75-million offer.
Since breaking into the majors in 2016, Story ranks as the fifth-best shortstop in the majors, according to FanGraphs WAR.