Javid had been widely expected to keep his job in the Cabinet shakeup. But a spokesman confirmed soon after that Javid had quit.
Javid's reported resignation on Thursday came over what a political editor claimed was a disagreement over his advisers, throwing Johnson's plans off kilter.
Javid was scheduled to deliver his first budget on March 11, after his November budget was scrapped due to a combination of ongoing delays to Brexit and the decision to hold a general election in mid-December.
Now his Conservative administration faces the even bigger challenge of negotiating a new trading relationship with the European Union while also seeking trade deals with the United States and other countries.
Johnson, who had wanted to minimize any disruption from the cabinet reshuffle, quickly appointed Javid's deputy Rishi Sunak, a loyal supporter of the prime minister who has often been put in front of the cameras to sell government policy.
"The prime minister said he had to fire all his special advisers and replace them with Number 10 special advisers to make it one team".
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Also sacked Thursday were Business Secretary Andrea Leadsom, Environment Secretary Theresa Villiers and and Housing Minister Esther McVey.
Johnson's office had earlier said the Cabinet changes would be modest, and apart from Javid most senior ministers kept their jobs.
Another elevation is that of International Development Secretary Alok Sharma, who will be the new Business Secretary; home secretary Priti Patel has been re-appointed in the Cabinet reshuffle.
But his first sacking - that of Northern Ireland minister Julian Smith, who, only a month ago - had helped broker the restoration of a government in the British province, had prompted criticism from politicians north and south with the border with Ireland.
As well as reworking his Cabinet, Johnson needs to appoint a new leader for the United Nations climate change conference that Britain is due to host later this year.
The government said Thursday that Alok Sharma, previously in charge of worldwide development, would become business secretary and also take charge of COP26.