The two pilots managed to eject just before impact, suffering minor injuries along with five others on the ground.
Several residents described hearing a loud explosion and looking out their windows to see the red and orange blaze.
In the confusion that followed, two men helped one of the bloodied pilots from the two-seat F18 Hornet move to safety.
"Oh, my God, I heard three really loud explosions, then the black smoke went up high in the sky," said 71-year-old Felissa Ezell, who lives in a townhouse near the crash site.
By evening, emergency crews were searching through the charred remains of the complex, where some 40 apartment units were damaged or destroyed.
No fatalities had been reported.
Seven people, including the pilots from nearby Naval Air Station Oceana, were taken to a hospital.
All except one of the pilots were released by late afternoon.
Virginia Beach Fire Department Capt.
Tim Riley said three residents remained unaccounted for late Friday.
"We don't know if we have working cell numbers, if they've traveled," Riley said. "We don't know if people are staying with other people."
He said crews had done an exhaustive search of about 95 percent of the apartment complex and would continue searching throughout the night.
"We consider ourselves very fortunate," he said.
The plane had dumped loads of fuel before crashing, though it wasn't clear if that was because of a malfunction or an intentional maneuver by the pilots, said Capt. Mark Weisgerber with U.S. Fleet Forces Command.
He said investigators will try to determine what happened. The jet went down less than 10 miles (16 kilometers) from Oceana.
Bruce Nedelka, the Virginia Beach EMS division chief, said witnesses saw fuel being dumped from the jet before it went down, and that fuel was found on buildings and vehicles in the area.
The plane not having as much fuel on board "mitigated what could have been an absolute massive, massive fireball and fire," Nedelka said.
"With all of that jet fuel dumped, it was much less than what it could have been."
The crash happened in the Hampton Roads area, which has a large concentration of military bases, including Naval Station Norfolk, the largest naval base in the world.
Naval Air Station Oceana, where the F/A-18D that crashed was assigned, is located in Virginia Beach. Both the pilots were from Virginia Beach, Weisgerber said.
The pilots included a student and an instructor. Weisgerber said he did not know how many times the student pilot had been in the air, but that the instructor was "extremely experienced."
Dozens of police cars, fire trucks and other emergency vehicles filled the densely populated neighborhood where the plane crashed.
Yellow fire hoses snaked through side streets as fire crews poured water on the charred rooftops of brick apartment houses. By late afternoon, the fire had been put out.
Residents of the apartment complex described a confusing scene and an apologetic pilot.
A fighter jet crashed in December 2008 while returning to Marine Corps Air Station Miramar after a training exercise in a San Diego neighborhood.
That crash killed four members of one family and destroyed two homes.
The Marine Corps said the jet suffered a mechanical failure, but a series of bad decisions led the pilot — a student — to bypass a potentially safe landing at a coastal Navy base after his engine failed.
The pilot ejected and told investigators he screamed in horror as he watched the jet plow into the neighborhood, incinerating two homes. A federal judge ordered the U.S. government to pay the family nearly $18 million in restitution.
Most flights from Naval Air Station Oceana are training flights, Weisgerber said.
"This is where the Navy teaches our F18 pilots for the very first time in flee-representative aircraft," he said.