The former UK prime minister said the move - which has now been scrapped - jeopardised the peace process.
The EU backtracked on a decision to use a Brexit deal clause to restrict exports of Covid-19 vaccines from crossing the Irish border into the rest of the UK late on Friday, following backlash from London, Dublin and Belfast.
The Nothern Ireland Protocol is designed to allow the free movement of goods from the EU into the territory, preventing the need for a hard border on the island of Ireland.
The EU initially triggered Article 16 of the protocol, which would have temporarily placed export controls on the movement of vaccines, in a bid to protect its own supplies amid its row with AstraZeneca over its supply contract.
Asked if the move was irresponsible, Mr Blair told Sky's Sophy Ridge on Sunday: “Yes, it was a very foolish thing to do and fortunately they withdrew it very quickly.”
The former PM said: "I was somebody who negotiated the Good Friday Agreement, it's brought peace to the island of Ireland and it is absolutely vital that we protect it.
"That's why what the European Commission did was unacceptable but, as you say, fortunately they withdrew it very quickly."
Michael Gove has also welcomed the EU having "stepped back" from triggering the article, which Northern Ireland's First Minister Arlene Foster described as an "incredible act of hostility".
Despite criticism from the World Health Organisation, the EU is pushing ahead with placing export controls on vaccines made in the bloc - including supplies of the Pfizer/Biontech jab which is produced in Belgium.
It comes amid a bitter row over the delivery of the Oxford-Astrazeneca jab into the continent.
Additional reporting by Press Association
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