After a standoff during a gruelling three-hour meeting in Downing Street, Greening walked out of the Cabinet.
Sajid Javid is also staying in position, though his brief changes from Secretary of State for Communities and Local Government to Housing, Communities and Local Government, making him the first United Kingdom minister with a housing department title since the 1970s.
Ms Greening said she thought it was the "right thing to do" to quit government rather than take the role at the Department for Work and Pensions (DWP).
The most prominent Conservative ministers reportedly under threat are Education Secretary Justine Greening, Party Chairman Patrick McLoughlin, Business Secretary Greg Clark and House of Commons leader Andrew Leadsom, who May went toe-to-toe with in the final round of the party's 2017 leadership contest.
And Jeremy Hunt reportedly dug his heels in to keep his job as health secretary after turning down the role of Business Secretary.
Even though May's de facto deputy, Damian Green, stepped down last month after he was found to have misled the public about pornography found on his work computer, she appeared to be in a stronger position than at any time since the general election in June.
May launched a long-awaited reshuffle of her Cabinet today, which nevertheless left most of her senior ministers in position.
Of the 23 ministers who make up the Government's top team, 34% attended fee-paying schools - up from 30% in May's first Cabinet in July 2016, social mobility charity The Sutton Trust has discovered. More ministerial appointments will be made tomorrow.
And Jeremy Hunt and Sajid Javid had additional roles added to their titles, with the Health Secretary taking on responsibility for social care and the Communities and Local Government minister having housing added to his remit.
Tory HQ tweeted congratulations to "new party chairman" Chris Grayling.
One minister who did leave the Cabinet was James Brokenshire, who resigned as secretary of state for Northern Ireland for medical reasons, telling May in a letter that he needed surgery to remove a small lesion in his right lung.
David Gauke was made the sixth justice secretary in eight years, prompting campaigners to voice fears that constant changing is delaying reform to prisons.
James Cleverly, a prominent backbencher, is the new Tory Party deputy chairman. Lidington will, however, likely take over Green's role in Brexit negotiations with the Scottish and Welsh governments.
Environment Secretary Michael Gove, International Development Secretary Penny Mordaunt, and International Trade Secretary Liam Fox all remain in the same jobs.
David Mundell remains Secretary of State for Scotland, and Alun Cairns stays on as Secretary of State for Wales.
Chief Secretary to the Treasury, Liz Truss, also stays in post.