The fire broke out about 4 p.m. beneath the far end of the pier at the three-story tourist hot spot, sending plumes of black smoke over lower Manhattan, the New York Daily News reported.
Firefighters attacked the flames with both firetrucks and boats, and the fire was knocked down by about 6 p.m., the newspaper said.
The fire occurred while the 4Knots Music Festival was under way nearby.
The mall was evacuated and there were no immediate reports of injuries, fire and police officials told The New York Times.
The smoke was so thick at times it obscured the Brooklyn Bridge, the newspaper said.
Jillian Miller, 24, of Brooklyn said people suddenly appeared in the accessories store where she was working and yelled there was a fire.
"We just ran," she said. "It was very dramatic."
Jenitza Rodriguez, 29, of Long Island said she was on the pavilion's second floor when the fire began.
"Black smoke was coming through the door," she said. "It smelled like an electrical fire."
The cause of the blaze had not been determined.