Workers began trickling back to offices and factories around China though a large number of workplaces remain closed and many white-collar workers will continue to work from home.
The death toll in mainland China from the novel coronavirus rose to 908 by the end of Sunday, surpassing the fatalities from the Severe Acute Respiratory Syndrome outbreak in 2003.
Meanwhile, data showed China's factory-gate prices snapped six months of year-on-year declines in January, but analysts do not expect the positive momentum to sustain amid economic risks from the coronavirus.
Leading decliners in Southeast Asia, Vietnamese shares fell 1.1% with financials losing the most. Joint Stock Commercial Bank for Investment and Development of Vietnam shed 5%.
"It is hard to see markets gaining further against the outbreak of coronavirus," Jeffrey Halley, market analyst at OANDA, wrote in a note.
"That is likely to be the theme of the week, as the economic damage is totalled up from the outbreak."
Singapore stocks closed lower for the second straight session, with financial heavyweights United Overseas Bank and DBS Group Holdings losing between 1% and 1.4%.
The city-state on Friday reported more coronavirus cases unrelated to previous infection or China travel, and raised its alert level to "orange".
Malaysian shares ended 0.8% lower, dragged by blue chips such as power utility Tenaga Nasional and Hong Leong Financial Group.
Investors now await fourth-quarter economic growth data due on Wednesday for clues about the domestic economy.
A Reuters poll shows growth likely slowed to its weakest since mid-2016 in the final quarter of the year on weaker private consumption and external demand.
Philippine shares gave up 1%, while Indonesian equities shed 0.8%.
Thailand stock markets were closed for a holiday.
By Arundhati Dutta
