No one was hurt and passengers on the San Antonio-bound flight were later put on another plane.
The pilot of the Airbus 319 reported a smoke condition, possibly from the cargo hold, Port Authority police said. Firefighters found no evidence of a fire, though.
The aircraft was at gate 66 in Terminal 2.
Scheduled to depart JFK at 6:20 p.m., flight 2164 ended up taking off at 9:46 p.m, according to Delta. It landed in San Antonio at 12:57 a.m. Monday.
“Prior to departure, the crew of Delta flight 2164 observed smoke in the rear of the cabin,” Delta said in a statement. “Customers were safely deplaned and maintenance is reviewing the cause. The customers arrived in San Antonio last evening on another plane. The safety of our customers and employees is our top priority.”