The MP for Orpington has also quit his role as minister for London so he can vote against the Brexit deal whenever it comes before Parliament. He said the UK was “barrelling towards an incoherent Brexit that is going to leave us trapped in a subordinate relationship to the EU”. He added it was “imperative” to “go back to the people and check they are content to proceed on this extraordinary basis”.
Mr Johnson voted to remain in the EU, while his brother Boris Johnson was a leading Brexiteer.
In a blog explaining his decision, he said: “It has become increasingly clear to me that the withdrawal agreement, which is being finalised in Brussels and Whitehall even as I write, will be a terrible mistake.
“Indeed, the choice being presented to the British people is no choice at all.
READ MORE: Live updates on Brexit
“The first option is the one the Government is proposing: an agreement that will leave our country economically weakened, with no say in the EU rules it must follow and years of uncertainty for business.
“The second option is a no-deal Brexit that I know as a transport minister will inflict untold damage on our nation.
“To present the nation with a choice between two deeply unattractive outcomes, vassalage and chaos, is a failure of British statecraft on a scale unseen since the Suez crisis.”
The former Transport Minister also called for a second referendum.
He said: “Given that the reality of Brexit has turned out to be so far from what was once promised, the democratic thing to do is to give the public the final say.
“This would not be about re-running the 2016 referendum, but about asking people whether they want to go ahead with Brexit now that we know the deal that is actually available to us, whether we should leave without any deal at all or whether people on balance would rather stick with the deal we already have inside the European Union.”
Mr Johnson’s family were quick to tweet their support for him, with his brother Boris – who resigned as Foreign Secretary in June in opposition to Theresa May’s Brexit plan – said he was united with Jo “in dismay at the intellectually and politically indefensible”.
He tweeted: “Boundless admiration as ever for my brother Jo. We may not have agreed about Brexit but we are united in dismay at the intellectually and politically indefensible.”
“This is not taking back control. It is a surrender of control. It does not remotely correspond to the mandate of the people in June 2016.”
The former Transport Secretary’s sister television personality Rachel Johnson, also tweeted: “Am hugely proud of my honourable and principled brother Jo who has put the interests of the country ahead of his political career.”
Downing Street thanked Mr Johnson for his work in government, but repreated there will not “under any circumstances” be a second referendum.
A spokesman said: “The referendum in 2016 was the biggest democratic exercise in this country’s history. We will not under any circumstances have a second referendum.
“The Prime Minister thanks Jo Johnson for his work in Government.”
Mr Johnson is the 14th minister to have resigned from the government since Theresa May held a snap election in June 2017.
His resignation came just hours after Mrs May’s de facto deputy David Lidington he hoped a deal would result in a “new dynamic” at Westminster, with MPs rallying behind the Prime Minister.
He said a UK-EU deal would involve “compromises, give or take on both sides”, but when faced with “product on the table” in the form of an agreement backed by all 28 governments, there could be a shift in attitude at Westminster.