Spokesman Dan Stessel says service was restored just before 5 a.m. Tuesday, nearly 17 hours after a derailment kept trains from using nine tracks.
Two cars of a Midtown Direct train carrying 300 people went off the tracks at 10:50 a.m. Monday. No one was injured.
Commuters faced crowded conditions in and out of New York on Monday night.
PATH trains and NJ Transit buses honored NJ Transit passes.