The so-called transparency mechanism gives EU countries powers to deny authorisation for vaccine exports if the company making them hasn't honoured existing contracts with the EU.
"The protection and safety of our citizens is a priority and the challenges we now face left us with no choice but to act," the European Commission said.
The controls will affect some 100 countries worldwide - including the UK, the US, Canada and Australia - but many others, including poorer nations, are exempt.
Britain on Friday expressed its "concern" after the EU also suspended terms of the Brexit deal allowing goods to flow across the Irish border.
The EU insists its controls are a temporary scheme, not an export ban. But the World Health Organization is among those criticising the move, saying it could have a knock-on effect around the world.
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