The incident was reported at 439 Lincoln Road around 2 p.m. when part of the ceiling and walls collapsed.
As the building was being demolished, a brick wall collapsed on the workers on the second floor which brought the roof down on top of them, the FDNY said.
The victims were pinned between the roof, the brick wall and the floor.
Rescuers had to shore up the building before they were able to pull out the victims.
"We had to prevent the building from falling further onto the workers," FDNY Deputy Assistant Chief Joseph Ferrante said. "We had to stabilize the workers' conditions, which we did by bringing in our EMS rescue medics to start IVs and to assess their conditions."
It would take an hour and 10 minutes to safely remove the first worker and hour and 20 for the second.
Both workers were removed from the collapse and were rushed to the hospital with serious injuries. They are now said to be stable.
Neighbors described a crash and a dust cloud then a massive response of fire vehicles and ambulances.
"I seen them, literally pull them out from the rubble," neighbor Maahad Hassan said. "It was weird, because it's the scaffolding on top and scaffolding consists of all the iron on top where it's covering the workers below. That thing fell, and it ripped out the brick wall of the other house with it."
VIDEO | NewsCopter 7 was overhead during the rescue:
Firefighters respond to scene of construction site collapse
There are active construction permits at the site for the vertical enlargement of the existing two-story building into a five-story building.
Inspectors with the Department of Buildings said their preliminary investigation has determined that the construction workers were performing demolition work on the second floor when the partial roof collapse happened.
A full stop work order has been issued at the scene. There had been several violations issued earlier this month for construction maintenance failures.
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