US parcel delivery company UPS confirmed the crash of the plane, which was en route to Cologne, Germany.
"I saw the plane suddenly dive down into the base and heard a huge explosion," said a nearby resident.
A government source familiar with the initial crash report said the plane had taken off from Dubai International Airport at 18:40 p.m. (1440 GMT) and was diverted to a military compound after reporting trouble.
The aircraft caught fire, hit a covered parking lot, then bounced and crashed, the source said, adding that there were no injuries on the ground.
The United Arab Emirates civil aviation authority said the bodies of the two crew members were recovered.
Saif Al-Suwaidi, general manager of civil aviation, told Dubai TV that flights had not been affected at Dubai's airport, the busiest in the Middle East.
"The pilot reported fire and smoke in the cockpit and was instructed to return to Dubai. After failing to land at the airport, the plane disappeared from radar screens and was found later (at the crash site)," Suwaidi said.
Smoke was billowing from the base, a Reuters witness reported. Initially, Al Arabiya television had reported the plane had hit a busy highway, but later reports indicated it did not hit the road.