The issue was discussed in a late-night phone call between Mr Johnson and EU Commission President Ursula von der Leyen. The Prime Minister had expressed “grave concerns” about the effects of EU vaccine export restrictions.
According to the Mail on Sunday, Mr Johnson told Ms von der Leyen the move could risk millions of UK pensioners not receiving their second jabs of the Pfizer vaccine.
The senior EU official appeared to concede the matter in a tweet late on Friday night.
Ms von der Leyen wrote: “Constructive talks with Prime Minister Boris Johnson tonight.
“We agreed on the principle that there should not be restrictions on the export of vaccines by companies where they are fulfilling contractual obligations.”
It followed widespread condemnation and a flurry of calls between UK and EU leaders after it emerged the EU considered using Article 16 of the Northern Ireland protocol.
Dubbed the “nuclear option,” the move would have allowed the EU to unilaterally act to avoid any “economic, societal or environmental difficulties”.
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“We’re out, and for Article 16 to have even been considered, the goodwill is sparing.”
Both the UK and EU have since agreed to “reset” relations.
Cabinet Office Minister Michael Gove said the EU accepts it had made a “mistake” over the move, which he said “would have meant the re-imposition of a border on the island of Ireland”.
The EU-UK vaccine row comes as the EU is calling for more British-made AstraZeneca jabs amid shortages.
The UK is aiming to vaccinate 15 million of the most vulnerable individuals in the country by the middle of next month.
