But Metro is still warning commuters to allow for extra travel time and to defer travel where possible.
The peak hour debacle also affected Melbourne's tram networks, with Yarra Trams reporting major delays, while Uber prices skyrocketed.
"We are currently experiencing delays to all lines due to an computer fault affecting the suburban area. Pls seek alternative transport," Metro Trains said on Twitter on Thursday.
"Passengers on-board services currently stopped between stations, please do not attempt to force doors open and alight from the train.
"Our technicians are currently working to rectify the problem and we are working to have services moving soon."
Yarra Trams also said "high demand" for trams was contributing to major delays.
Earlier, Metro Trains warned of major delays.
