Flames quickly tore through the buildings on Ogden Avenue in the Highbridge section after breaking out just after 1:10 a.m.
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Video from the scene showed heavy flames shooting from the structures.
It took nearly 200 firefighters and several hours to bring the blaze under control.
Residents from adjacent apartment buildings were evacuated as a precaution.
One woman told Eyewitness News she was able to run out of her apartment with her dog.
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"It was smoky," said Laura Mitchell. "Black smoke. And the flames were coming out of the next door apartment... like, all holes. Coming from the windows, the downstairs doors, everywhere... the top."
Theresa Jones came to check on her sister, who lives next to the fire scene.
"It's devastating," Jones said. "I'm glad that the building was empty and no one was in there so no one could get hurt."
Fortunately the inferno did not spread beyond the two homes, and no injuries were reported.
While the homes were empty, some neighbors said they have seen squatters there in the past.
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"With that amount of fire in the middle of the night, we have our fire marshals investigating the cause," said FDNY Chief of Fire Operations John Esposito. "They will determine what started it."
Building inspectors were heading to the scene to assess the stability of the damaged buildings.
They will likely have to be demolished.
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