The EU Commission said the pair “shook hands” on the deal, which is set to unlock trade talks later this month, and that it trusts the UK to be as good as its word.
Eurocrats sought to clarify the situation after David Davis implied in a television interview that the text was not legally binding on the UK and could be altered.
That declaration provoked outrage from the Irish Government, which had pushed hard for concrete promises on the border situation, with Dublin insisting it considered the agreement bullet proof.
The Brexit secretary has since insisted that his words were misrepresented by the media and that he had meant to say the agreement was not only legally but also politically binding.
Taoiseach Leo Varadkar responded this morning by saying he was “delighted” by the clarification, with the row having temporarily threatened to overshadow Downing Street’s euphoria at clinching a deal.
Mr Davis’ remarks could also have caused trouble for the UK at this week’s EU Council summit, where the 27 other leaders still have to sign off on sufficient progress for trade talks to begin.
Asked about the confusion today, a Commission spokesman said: “Formally speaking the joint report is not legally binding because it is not yet the Article 50 withdrawal agreement.
“But we see the joint report of Michel Barnier and David Davis as a deal between gentlemen and it is the clear understanding that it is fully backed and endorsed by the UK Government.”
He emphasised: “President Juncker had a meeting with Prime Minister May last Friday morning to ascertain that this is the case. They shook hands.
“It’s now for the European Council to decide if sufficient progress has been made to allow the negotiations to proceed to the second phase.”
Pressed on why such questions had arisen just days before Friday’s crucial EU summit, he sarcastically added a dig at Mr Davis: “I don’t think I’m creating the confusion.”
The agreement was attacked by some backbench Brexiteers, who saw it as a betrayal of the referendum result, but was backed by leading Leavers including Boris Johnson and Michael Gove.
In particular they were enraged by the Brexit bill, calculated at around £40 billion, and a commitment to continue “regulatory alignment” with Brussels if an alternative solution to the Irish border question cannot be found.
There has been confusion within the Government over whether the agreed sum of money is binding, with Chancellor Philip Hammond suggesting Britain will hand over the cash even if it doesn’t get a trade deal.
EU leaders will include a line in their conclusions on Friday calling for the joint agreement to be drawn up into a legal document, but the pact will not be signed and come into force until just before Britain leaves in 2019.
They will say: “Negotiations in the second phase can only progress as long as all commitments undertaken during the first phase are respected in full and translated faithfully in legal terms as quickly as possible.”