It comes eight months after Brussels issued a similar derogation for medicines.
Brussels on Monday announced that it will issue a temporary waiver to allow citizens and businesses in Northern Ireland, Ireland, Cyprus and Malta to import veterinary medicines from Britain.
Brexit meant that Dublin, Nicosia and Valletta — whose supplies of medicines had historically been supplied through or by the United Kingdom — were restricted from importing such products from the UK.
Northern Ireland, which is still part of the bloc's Customs Union in order to avoid the creation of a hard border with the Republic of Ireland, is also affected.
"We have listened carefully to the concerns raised by stakeholders, particularly those in Northern Ireland. We understand those concerns. And that is why we are acting today," Maroš Šefčovic, Vice-President of the European Commissioner for Interinstitutional Relations, told reporters.
"By extending the current arrangements to December 2025, we are giving ample time to adapt.
"This is a practical solution to a practical problem. And it underlines our genuine commitment to engaging constructively with the UK to find agreed solutions around the Protocol."
This announcement comes eight months after the European Commission issued a similar derogation to ensure the long-term supply of medicines to the three EU nations and Northern Ireland.
British Foreign Minister James Cleverly said on Twitter that he welcomes the announcement "which provides greater certainty for the veterinary medicines industry in Northern Ireland."
"We will continue to look for long-term solutions on the Protocol, including on vet meds, to provide political stability in NI," he added.
Brussels and London have resumed negotiations over outstanding issues that have marred the implementation of the protocol after talks broke down for several months in February when the UK published legislation that would substantially override their legal obligations under the agreement.
Sticking points include the number of customs and regulatory checks on goods moving from Britain to Northern Ireland, the role of the European Court of Justice, steel tariffs, state aid, and the UK's demand for a dual regulatory system for goods within Northern Ireland.
Both sides have meanwhile started legal actions against the other over Brexit.
Brussels accuses London of failing to comply with the applicable customs requirements, supervision requirements and risk controls on the movement of goods from Northern Ireland to Great Britain.
It also says the UK government has failed to implement EU rules on Value Added Tax (VAT) for e-commerce and failed to notify them that they will implement EU rules related to indirect taxes, in particular on alcohol and alcoholic beverages.
The UK has meanwhile launched a formal appeal against its exclusion from EU scientific research programmes.
Šefčovic told reporters on Monday that he "hope(s) that can carry today's positive announcement into other areas of our discussion."
"I am convinced that there is a window of opportunity for a positive outcome, for the benefit of people and businesses in Northern Ireland. My team and I will continue working around the clock to that end," he said.