Commemorations took place at 10am in all major cities, but were particularly poignant in Wuhan, where the disease was first detected in December.
Wuhan was lauded as a “heroic city” by the country’s communist leaders during the remembrance service.
People have gradually been allowed to travel in and out of Wuhan under strict conditions. The quarantine on the city is to be formally lifted on Wednesday.
In Beijing, President Xi Jinping led other top officials, all dressed in black suits with white carnations, as they bowed before a flag at half-mast in the leadership compound of Zhongnanhai.
On Saturday, China reported one new confirmed case in Wuhan and 18 among people arriving from abroad, along with four new deaths, all in Wuhan.
China now has recorded a total of 81,639 cases and 3,326 deaths, although those figures have been questioned by critics.
The State Council, China’s Cabinet, ordered that national flags be flown at half-mast around the country and at Chinese embassies and consulates abroad, and the suspension of all public recreational activities.
The horns of automobiles, trains and ships joined in what the official Xinhua News Agency called a “wail in grief” for three minutes. China has held such moments of silence in past, often to mark World War II-era atrocities by Japan, but rarely on a national scale.
The commemoration also comes on the traditional Qingming festival, when Chinese visit the graves of their ancestors. Officials have banned such observances this year to avoid large gatherings that might contribute to a feared second wave of infections.
More than 3,000 health care workers contracted Covid-19 and the government says 14 died of the disease. Among them was doctor Li Wenliang, who was threatened with punishment by police after publicizing news of the outbreak but has since been listed among the national “martyrs.”
Coronavirus: Everything you need to know