Suffolk County Police said a passerby in the parking lot heard the girl crying from inside the car, where windows were rolled up and temperatures indoors reached an estimated 120 degrees.
Police said Melvin Marroquin, the girl's father, returned to the 2000 Nissan Frontier about 10 minutes after authorities arrived at the shopping center in Huntington.
Marroquin, 30, was arrested and charged with child endangerment and second-degree reckless endangerment. He is scheduled to appear before a judge in Islip, N.Y. on Friday.
The girl was reportedly lethargic when rescued from the car and was taken to a nearby hospital for treatment. She will be released to her mother, police said.