It turned out to be a training device that looked like a real bomb.
The device was left inside the car by a salesman who works for I Robot, a company that develops robots to disarm bombs.
He had been planning to use it for a sales demonstration.
It was found by a worker cleaning the car at the Budget Rental Car building.
The discovery prompted evacuations of of the Budget building and parking lot, as well as the nearby Dollar Rental Company.
The Port Authority also evacuated a large area of the airport, and the Air Train was suspended.
After dropping off the car at the Budget building, the man boarded a flight to Boston.
Law enforcement officials met him when the plane landed at Logan Airport.
After speaking with the man, and representatives for the company, the training device was deemed safe.
All airport operations were back to normal as of 4:10 p.m.
But the scare caused delays for passengers trying to return their vehicles before catching flights.
"It's a little unnerving. Despite some of the craziness, you're just trying to take care of your own situation," said traveller Jon Montgomery.
"You never want to hear about a suspicious package at any location, let alone one where you might find yourself."
Meanwhile, Massachusetts state police say they are working with various federal agents who are questioning the United Airlines passenger who left the car behind.
Authorities did not identify the man because he has not been charged with a crime.
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