The controversial chief adviser was pictured exiting the front door of Number 10 on Friday evening carrying a large cardboard box, following the resignation of his Vote Leave ally Lee Cain, the PM's director of communications.
The pair will work the rest of their notice period - until the end of this year - from home, it is understood, following a bitter dispute in Number 10, allegedly relating to the appointment of the PM's new press secretary Allegra Stratton.
Senior Tory MPs have now called on the Prime Minister to use his departure to "reset the Government" following complaints the party and Parliament were not being listened to during Mr Cummings' time as senior adviser.
Sir Edward Lister was announced as the interim chief of staff pending a permanent appointment.
Listen to Robert Peston explain the Number 10 meltdown in his politics podcast:
The dramatic events have come with Brexit headed to a crucial phase next week, as London seeks a trade deal with Brussels ahead of the end of the transition period on December 31.
The Sun reported there was a “shouty” confrontation between Mr Johnson and Mr Cummings over the ousting of Mr Cain and that a “livid” Prime Minister wanted both out “sooner rather than later”.
The BBC reported Mr Cummings’s departure had been brought forward given the “upset in the team” and that the PM wanted to “clear the air and move on”.
Former Brexit secretary David Davis told BBC Breakfast on Saturday many within No 10 had "turned on" Mr Cummings.
He said: "It is said... people ranging from Allegra (Stratton) - the new spokesman for the Prime Minister - right through to his (Mr Johnson's) fiancee, Carrie, turned against him.
"The relationship with the Prime Minister fell off a cliff. And once that's gone, it's gone."
Despite the controversy surrounding the two departures, Mr Cummings has said his “position hasn’t changed since my January blog”, in which he said he hoped to be “largely redundant” by 2021.
Video report by ITV News Political Correspondent Daniel Hewitt
Senior Tory MP Sir Bernard Jenkin said it was time to restore “respect, integrity and trust” to the relationship, elements which had been “lacking in recent months”.
The Daily Telegraph said tensions within No 10 were running high, with Mr Cummings accused of briefing against the Prime Minister.
The newspaper reported Mr Cummings was said to have told colleagues Mr Johnson was “indecisive” and that he and Mr Cain relied on Cabinet Office minister Michael Gove for clarity.
It was also suggested the PM was angered by claims a faction headed by Mr Cummings and Mr Cain had been “briefing against him” and his fiancee Carrie Symonds.
Mr Davis said the photos of Mr Cummings leaving Downing Street could help "reset government".
He told BBC Breakfast: "The photograph will last the weekend and people will remember it, but it's not the key.
"And at one level, as I said, Boris will want to reset Government and in a sense, that photograph does part of the resetting for him."
Meanwhile, shadow health secretary Jonathan Ashworth highlighted the strain being heaped on the NHS and the public by Covid-19 while “Downing Street is paralysed by the soap opera of these self-indulgent spin doctors”.
“It’s pathetic,” Mr Ashworth said.
The Prime Minister’s official spokesman, James Slack, who will replace Mr Cain in the new year, insisted Mr Johnson is not being distracted from the national crisis by the row.
“What the Prime Minister and the Government are focused upon is taking every possible step to get this country through the coronavirus pandemic,” he said.