The Prime Minister had been expected to keep Mr Javid in post and news of his resignation shocked Westminster.
Johnson's aides had previously played down suggestions, based on Johnson's senior adviser Dominic Cummings' well-publicised desire to see a radical reorganisation of government, that there would be major changes.
Javid was only appointed in July past year, making him one of Britain's shortest-serving chancellors.
Universities and science minister Chris Skidmore said he would be spending more time with his family due to a "promotion in the reshuffle".
Johnson had asked Javid to fire and replace all of his special advisers, British media reported.
The chancellor said no self-respecting minister would accept those terms.
And there will be a joint pool of advisers serving No 10 and No 11.
Also on their way out is Geoffrey Cox, the Attorney General whose advice to Theresa May was crucial during her failed Brexit process.
Over the course of the day, Johnson sacked a number of his ministers.
The Cabinet reshuffle saw the departure of key Brexiteer politicians from the frontbench, including Business Secretary Andrea Leadsom and Environment Secreatry Theresa Villiers.
Shadow Chancellor John McDonnell said: "This must be a historical record with the government in crisis after just over two months in power". I wonder if Number 10 hasn't made a miscalculation here.
Former Tory leadership contender Ms McVey said she was "very sorry to be relieved of my duties".
But the finance minister's resignation - which some commentators said might have been sought by Johnson's team - because of a dispute over Javid's advisers added to the picture that the prime minister will not tolerate dissent in his government.
"He wants to promote a generation of talent that will be promoted further in the coming years".
Mr Javid was also British home secretary from 2018 to 2019.
George Freeman said he was "on my bike" after losing his transport job.