It followed a "network-wide failure" that caused delays, a Metrolink spokeswoman said.
There had been a communications failure between the control room in the depot and trams on the network, she added.
Metrolink boss Danny Vaughan said: "I'd like to apologise once again and thank passengers for their understanding."
There is no indication the fault was caused by hacking.
In May, the tram network was shut down because control room staff lost visible sight of trams.
All tram services have resumed in Greater Manchester after the whole network shut down on Saturday following a communications problem.