The man is believed to have contracted the virus in Guangzhou, a busy city in the Guangdong province bordering Hong Kong and one of the territory's major poultry suppliers.
He died Thursday, nine days after being hospitalised after developing fever and pneumonia on Feb 22.
The ban, which will be reviewed in three weeks, comes as a precautionary measure following a meeting between health officials. Border health checks have also been stepped up.
A health department spokesman said that though there had not been an avian influenza outbreak in Guangdong, the ban was deemed necessary to allow time for an investigation.
The case in Guangdong has raised fears that human infections are inevitable in Hong Kong, which has so far avoided any cases in this outbreak.
Hong Kong witnessed the first-ever human cases of the current bird flu strain in 1997 when 18 people were infected, six of whom died. The outbreak was the first known instance of the virus jumping the species barrier.
Since then, the territory has set up strict regulations for farming and selling chickens, including vaccinating poultry at farms and regular clean-up days at wet markets.
In recent weeks, a number of wild bird have been found dead, with the H5N1 virus heightening fears that Hong Kong will soon record its first human victim.