Car traffic outside the tunnel was diverted to local streets in New Jersey.
Commuter buses were held at Manhattan's Port Authority Bus Terminal, where thousands of commuters fumed.
Police were investigating a suspicious item. That item was a bottle. Investigators determined that the bottle was harmless.
The incident resulted in delays of up to two hours.
Officials at the bus terminal told Eyewitness News reporter N.J. Burkett that operations returned to norma around 9:00 p.m.
Even at that hour, residual traffic problems continued to plague the city at every Hudson crossing. Traffic was backed up outside the Holland from Canal to 14th Street.
It's the second time this week that the tunnel was closed for an investigation.
On Wednesday, tunnel traffic was diverted to local roads for several hours due to two bottles filled with an unidentified liquid that were found not to be hazardous.
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