The incident happened just before 2:30 a.m. Sunday on Park Avenue in the Fort Greene section, and it was caught on surveillance camera.
The suspects entered the location, produced a silver firearm, removed cigarettes and money from the cash register and fled on foot.
The store owner, Hasan Lsamdi, says the man threatened to kill him and forced him and a customer to the floor.
"He tell me, 'If you doing anything, I kill you,'" Lsamdi said. "I ask him, 'What are you, playing with me?' He tell me, 'No, I not to play. I am serious.'"
Lsamdi, who served in the Jordanian army before coming to the U.S., was not injured. He said when someone has a gun and you don't, you do what they say.
"He tell me, 'If you talk too much, I kill you,'" he said. "I tell them, 'Okay, what you need now?' He said, 'I need money.' I tell him I can't give him money. He tell me to go outside. I go outside, he take money, he take cigarettes. That's it."
Lsamdi says he is changing the way he does things during the overnight hours, which he has been working for about a year. He says he typically will let people into the store to make their purchases. Now, he says they can use the window instead.
Anyone with information is asked to call Crime Stoppers at (800) 577-TIPS (8477). All calls are strictly confidential.