The team made the announcement Thursday night, saying Gonzalez will have his patella tendon repaired.
It's been an injury-riddled year for Gonzalez, who is on the disabled list with not only an aching left knee but a sprained right ankle. He was out earlier this season after doctors found and removed a small tumor in his left index finger.
With all his ailments, Gonzalez struggled at the plate. He hit .238 with 11 homers and 38 RBIs.
The last-place Rockies are already missing All-Star shortstop Troy Tulowitzki, who will undergo season-ending hip surgery Friday in Vail, Colorado.