The disruptions were caused by the derailment in Brockville, Ont., of a CN freight train early Thursday.
Thousands of passengers have been transported by bus through the routes.
Via Rail tweeted Friday afternoon that trains 668 and 669 would operate on the Toronto-Montreal route on Friday night.
No one was injured when 25 cars on a 68-car CN freight train derailed.
The train was hauling two loaded automobile carriers, five cars containing carbon powder and 13 unloaded fuel tank cars.
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