Javid's resignation was a surprise moment during Thursday's reshuffle and came after he refused to cave to demands from Downing Street to sack his entire team of aides.
The resignation comes just two months after Mr Johnson's sweeping election victory in December and four weeks before Mr Javid was due to deliver his first budget. His resignation shakes the government as it faces the challenge of negotiating a new relationship with the 27-nation European Union by the end of this year. That involves ambitious infrastructure plans, including a 100 billion-pound ($130 billion) high-speed railway connecting London to central and northern England.
Johnson, who had wanted to minimise any disruption from his long-planned cabinet revamp, on Thursday quickly replaced Sajid Javid with his deputy Rishi Sunak, a loyal supporter of the Prime Minister who is often put before the media to sell government policy.
The PM said he had to fire all his special advisers and replace them with No 10 special advisers to make it one team.
Johnson had not been expected to change the biggest-hitting posts in his government. His office said Foreign Secretary Dominic Raab, Home Secretary Priti Patel, Justice Secretary Robert Buckland and Cabinet Office Minister Michael Gove were all staying.
Smith was the first minister to lose his job in the reshuffle and was later joined by business minister Andrea Leadsom and environment minister Theresa Villiers. Others were promoted, including Suella Braverman to the position of attorney general and Anne-Marie Trevelyan to the post of worldwide development secretary.
Julian Smith, the Northern Ireland secretary, is another shock sacking after overseeing the restoration of the power-sharing government in Stormont last month - a notable achievement considering a resolution could not be found in the three years prior. The summit, known as the 26th Conference of the Parties, or COP26, is scheduled to be held in Glasgow in November.
Planning for that has gotten off to a rocky start, with Johnson last week firing Claire O'Neill, a former British government minister appointed a year ago to head up the event.