The problems, near Newark's Penn Station, started Tuesday afternoon.
NJ Transit said dispatchers were prevented from moving trains using the illuminated signals on the tracks.
All Northeast Corridor, North Jersey Coast Line and Amtrak trains were required to stop at each signal and request verbal permission to proceed.
Commuters faced standing-room-only conditions.
Officials had feared delays on Northeast Corridor and North Jersey Coast Line trains of up to 30 minutes Wednesday. However, the problem was fixed by 4:45 a.m.
NEW YORK AND TRI-STATE AREA NEWS
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