Police evacuated hundreds of people from the station and the adjacent Oculus building after a bomb-sniffing dog got a hit on the bag, which was left on the last car of a train from Hoboken, police sources said.
Port Authority cops on the scene cleared the Lower Manhattan site Oculus just before 3 p.m.
At about 4:45 p.m. a spokesman for Mayor de Blasio tweeted that the police had given the all-clear.
“NYPD Bomb Squad has examined and cleared the package. No danger,” press secretary Eric Phillips said.
All service was restored by 5 p.m.