The incident happened around 10:30 p.m. Monday on Remsen Avenue near Avenue D in Canarsie.
Investigators say one of the men entered the gas station booth, while the other held the officer and an attendant at gunpoint.
As they fled the scene, the officer reportedly identified himself and demanded the suspects drop their guns. When they didn't, he fired a shot and struck one of them in the torso.
That suspect was pronounced dead at Brookdale Hospital.
Police are still looking for the second suspect.
Anyone with information is urged to call Crime Stoppers at 1-800-577-TIPS.
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