All weekday trains resumed on the Geelong line on Monday after eight COVID-19 cases in the past fortnight forced about 300 V/Line employees into isolation causing major disruptions.
V/Line on Sunday announced trains would resume from the first service on the Geelong line with all trains to run between Southern Cross and Waurn Ponds stations.
Trains to Warrnambool and all stations in between will also resume.
Full trains are also running on the Ballarat, Bendigo, Gippsland and Seymour lines.
Full services resumed to a Saturday timetable on the Geelong line on Friday for the AFL grand final eve public holiday.
Normal weekend services resumed on Saturday and Sunday.
“We apologise to passengers who were making permitted journeys over the last two weeks for the disruption to their journey and thank them for their continued patience and understanding while we worked to return train services across the network as quickly and safely as possible,” a V/Line spokesperson said.