Bulawayo Mayor Thaba Moyo told the BBC the “big flush” would keep pipes wet and so prevent them getting clogged up.
A severe drought and years of poor maintenance have meant Bulawayo residents often go without running water for three days at a time.
The first synchronised flush took place at 19:30 local time (17:30 GMT).
Council workers had visited townships warning people that they risked a fine if they failed to take part.
Mr Moyo said the lack of water in the sewage pipes had already led some to burst.
Many of the city’s million residents are believed to have flushed at the appointed hour.
“I made sure my wife and children flushed the toilet at 19:30 to avoid blocking our own toilet. So far, the flushing of toilets was a success here in Cowdray Park township,” one resident, human rights activist Dumisani Mpofu, said.
According to the Associated Press, the synchronised flush will now take place at the same time twice a week – on Mondays and Thursdays – though residents will of course be able to flush their toilets at other times too.
The BBC’s Thabo Kunene, in Bulawayo, says that most houses in the city, even in townships, do possess toilets which flush, unlike in many African countries.
But he says that due to a lack of water, many people have been using buckets of water instead.
The proposal has had a mixed reception in the city.
“Our leaders are a joke,” said Petros Ncube. “What they should be doing is finding money from donors to buy new sewer pipes,” he said.