European Commission and UK negotiators struck the accord, which replaces the EU's "backstop" with new arrangements for the Irish border, earlier in the day.
"The European Council endorses the Agreement on the withdrawal of the United Kingdom of Great Britain and Northern Ireland from the European Union and the European Atomic Energy Community," the European Council conclusions read.
"On this basis, the European Council invites the Commission, the European Parliament and the Council to take the necessary steps to ensure that the agreement can enter into force on 1st November 2019, so as to provide for an orderly withdrawal."
Speaking at a press conference after the meeting of leaders, EU chiefs expressed regret at Britain's departure, but relief that the deal had been struck.
"It's a little bit like an old friend that's going on a journey or adventure without us, and we really hope it works out for them, but I think there will always be a place at the table for them if they ever choose to come back," Ireland's Leo Varadkar said.
Chief negotiator Michel Barnier told reporters: "I too very much regret Brexit. I deeply regret it. However, we respect it, it was a sovereign choice of a majority in the UK. I have a sort of Gaullist tendency myself, but I have a great deal of admiration for the UK... We will never forget the solidarity shown by the British in our darkest hour."
Asked what his message was to the 48 per cent of British voters who supported remain, European Council president Donald Tusk said: "I regret that it was only 48 not 52."
His colleague, European Commission president Jean-Claude Juncker however added: "I would like to say to the 48 that they were right."
Mr Barnier added: "I want to underline one point: while the subject matter in the negotiating room may very often have been technical, about customs, goods, borders, what has mattered above all has been for me and my team been people in Ireland and Northern Ireland. For me what really matters are the people of Ireland and Northern Ireland and peace on the island of Ireland."
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