The commercial hub has had six of the country's 16 confirmed cases of the H7N9 strain, found in humans for the first time, with four deaths. The other two fatalities have been in the neighbouring province of Zhejiang.
Shanghai had culled more than 20,500 birds at an agricultural market in a western suburb by Friday, after the virus was found in pigeons, and the government announced a ban on live poultry trading and markets.
A uniformed worker sprayed disinfectant from a tank on his back at one local market in central Shanghai Saturday, where two booths selling live poultry were dark, and cages empty.
"All trading has stopped because of bird flu. The seller has gone home because he has nothing to do," said a seafood vendor.
But eggs, including pigeon eggs, remained on sale, as well as fresh and frozen poultry meat, as officials encouraged people to cook them well.
"People are worried," said Yan Zhicheng, a retired factory manager who like many elderly people in Shanghai makes a daily trip to market.
"Shanghai people eat a lot of duck and chicken. Now we can't touch them."
Prices of vegetables and seafood have surged since the ban was announced at a government news conference on Friday afternoon, local television reported.
Shanghai would compensate people involved in the poultry industry, but the level of pay-outs had yet to be set, a city government spokesman told the news conference.
There was no evidence of human-to-human transmission in Shanghai, city officials said.