Sheriff's Lt. Clayton Lisk said the man's body was found in the Jamul area Sunday afternoon following a search-and-rescue effort.
The owner of Skydive San Diego told reporters the victim was practicing a maneuver called tracking when he collided with his jump partner's knee or leg.
Buzz Fink said the victim's parachute was never deployed. The other jumper involved in the collision was not injured and was able to land in the drop zone.
Fink said the victim, who was in his 20s, was an experienced skydiver who had completed more than 1,000 jumps.