The collision occurred at about 11 am yesterday, Federal Aviation Administration spokesman Ian Gregor said.
Both planes - a twin-engine Sabreliner jet and a single-engine Cessna 172 - were approaching Brown Field, Gregor said.
The aircraft caught fire when they hit the ground and broke apart, said Nick Schuler, a division chief with the California Department of Forestry and Fire Protection.
"It appears it was a very violent crash, as you can tell by both aircraft being in multiple pieces," Schuler said.
More From This Section
The Sabreliner crashed on a grassy slope and the Cessna fell within the bounds of the San Diego National Wildlife Refuge.
Crews extinguished several brush fires where the planes came down. One firefighter was taken to the hospital after he suffered a heat-related injury, Schuler said.
Brown Field, a former Naval auxiliary air station, is in the Otay Mesa area southeast of downtown San Diego, near the border with Mexico.