The Bureau of Meteorology cancelled the statewide severe weather warning on Sunday morning and lifted a number of prepare-to-evacuate warnings.
Rivers levels are dropping across the state, the bureau says, but a number of moderate flood warnings remain in place, including for the Yarra, Ovens and King rivers.
Premier Daniel Andrews will visit the state's flood zones on Sunday.
"There is still work to do in a number of northeastern communities which are of significant concern to us, although it does seem we've had good news in recent hours," Mr Andrews told reporters in Melbourne.
"We've had the amount of rain that was forecast but luckily some parts of eastern Victoria received much of what had been predicted to fall in the metropolitan area."
The premier said there was concern for about 15 homes in Wangaratta, which could be inundated on Sunday.
The highest rain totals were at Mt St Leonard, near King Lake, with 228mm, Strathbogie with 221mm and 200mm at Sevens Creek, where there was major flooding on Friday morning that resulted in some evacuations.
The SES received about 2500 calls for help in the past 36 hours, the most in the state's northeast, 900 of them from 4pm (AEDT) on Saturday.
Seventy-three homes had water in them by Sunday but only a small number had it above the floorboards, Mr Andrews said.
Emergency Commissioner Craig Lapsley said people needed to remain vigilant because large amounts of water was still moving down rivers.
"The water will move through and that will take, in some cases, hours or days to do so," he said.
"The message to the Victorian community, particularly in northeast Victoria or Gippsland, is stay tuned about your river system and what it will do in your backyard."
Melbourne escaped relatively unscathed despite having more than a month's rain delivered over two days.
"In the last 24 hours, Melbourne's recorded its highest rainfall since 1992," senior forecaster Kevin Parkin said on Sunday.
"It was certainly a wet day out in the eastern suburbs, with rainfall over the last couple of days in excess of 100mm with lots of flash flooding and rises in river systems."
Clayton South recorded the highest rain in the city with 71mm, while the Dandenong Ranges had 90mm.
There have been a number of rescues for people trapped in cars in floods, the latest in Melbourne on Sunday when a man tried to drive through a swollen creek in Williamstown.
The bureau is keeping close eye on a weather system likely to hit the state on Tuesday or Wednesday, bringing further heavy falls up to 50mm in Gippsland and eastern Victoria.
