© Stefan Rousseau/PABoris Johnson arrives in Downing Street as he reshuffles his cabinet
Esther McVey was also removed as housing minister, and Chris Skidmore as universities minister, adding to the churn in two roles with a recent history of high ministerial turnover.
One surprise was the sacking of Nusrat Ghani as a junior transport minister. Ghani had been tipped to become the new minister for HS2, but tweeted that she would now "get to spend more time with family and constituents".
She was one of two junior transport ministers sacked. "On my bike," tweeted the other, George Freeman.
While widely briefed, the dismissal of Smith as Northern Ireland secretary despite his overseeing the restoration of the Northern Ireland assembly following three years of deadlock, prompted some anguish, with the nationalist SDLP saying it showed "Johnson's dangerous indifference to us".
"Serving the people of Northern Ireland has been the biggest privilege," Smith tweeted, having arrived at parliament to see Johnson, and telling reporters he expected to go.
Leadsom, the business secretary, who first became a minister under David Cameron, had been widely expected to lose her job.
She tweeted: "It has been a real privilege to serve in government for the last six years, and in @beisgovuk for six months. I now look forward to focusing on my constituents and on my 20+ year campaign to see every baby get the best start in life." Leadsom is a longtime campaigner for early intervention in children's lives.
Cox, the attorney general, had been due to answer ministerial questions in the Commons on Thursday morning, but was replaced by the solicitor general, Michael Ellis. Cox later tweeted his hugely loyal letter to Johnson, praising his delivery of Brexit.
Villiers, the environment secretary since July, was somewhat less phlegmatic in a Facebook post confirming her departure, beginning: "What the Prime Minister giveth, the Prime Minister taketh away: just over six months ago."
McVey, who was work and pensions secretary under Theresa May but resigned over Brexit, returned to the government as housing minister, but has now been sacked. She was the the 10th occupant of the role inside 10 years.
She tweeted: "I'm very sorry to be relieved of my duties as housing minister I wish my successor the very best & every success."
Universities ministers have also changed repeatedly in recent years, and the latest one, Skidmore, departs after only five months.
Skidmore tweeted to say he had got "a promotion in the #reshuffle to be a better Dad".
Smith's dismissal could prove the most controversial, given his success in restoring the assembly, and his reputation as a diligent secretary of state amid a potentially difficult time for Northern Ireland due to Brexit.
There had been reports that No 10 had been concerned at the way some elements of the Stormont deal were pushed through, particularly those relating to retrospective investigations into the actions of British troops.
Colum Eastwood, the leader of the SDLP, tweeted: "Sacking the most successful SoS in a decade shows Johnson's dangerous indifference to us."
One staffer at the Northern Ireland Office in Belfast said colleagues had been crossing fingers for Smith to be kept on as secretary of state, saying he was the most engaged, competent boss they had had in a long time.
After seeing those to be dismissed in his House of Commons office, meaning they did not first have to brave the waiting media, Johnson moved to Downing Street to continue the reshuffle.
The prime minister has, for now, set aside plans for a radical overhaul of Whitehall machinery in favour of a modest shake-up.
Sajid Javid, the chancellor, who has clashed with Johnson's chief adviser, Dominic Cummings, appears safe, with Rishi Sunak also left in place as chief secretary to the Treasury.
Jobs due to be filled include culture secretary, a job which Nicky Morgan made clear she would only do for a few months when Johnson handed her a peerage after the general election.
As well a new HS2 minister, Johnson is also due to name one to oversee the COP 26 climate conference.
Comment: Despite choosing to keep Javid on, he later quit after refusing Downing Street's request to sack his advisors: See also: