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The decision was taken by the EU's executive commission, which said the 25-nation bloc "only imports small quantities of meat from ostriches from South Africa" and that the country had already suspended such exports.
"However, in view of the risk of animal disease introduction into the EU, a commission decision is appropriate," it said in a statement announcing the suspension.
South Africa, the world's largest exporter of ostrich meat, began slaughtering around 30 000 ostriches on Tuesday to contain the outbreak of avian influenza.
The European Commission said the South African strain of bird flu was less potentially harmful to human health than a strain in Asia that has killed 24 people this year.
In principle the EU suspension will remain in force until January 1 next year, but will be reviewed periodically by EU health experts to see if it should remain in force until then.
"In the meantime, the South African authorities should provide the EU with detailed information on the disease situation and the measures taken to bring the disease under control," the commission said.
