Spokesman Dan Stessel says that means normal service has resumed between Newark and New York City, albeit with lingering delays that are quickly clearing out.
Amtrak service is also is running normally.
Officials say partial service was restored on one track around 2:30 p.m., and on the other about two hours later.
NJ Transit suspended rail service in both directions between Newark and New York City earlier in the day due to overhead wire damage near the Portal Bridge in Secaucus. It's not clear what caused the damage.