Sparks flew with Mr Johnson visibly rattled after being dealt blow after blow over the refurbishment of his Downing Street flat, which he claims to have paid for himself.
Mr Johnson was so furious that his final response to Sir Keir during the session was described by the Labour leader's spokesperson as the prime minister's "Kevin Keegan moment" (bottom video on this page).
The scene was set when an investigation into the refurbishment of Mr Johnson's flat was launched by the Electoral Commission just an hour before Prime Minister's Questions.
Watch PMQs in full:
With Mr Johnson on the backfoot, Sir Keir began his questions by asking the PM if he really remarked that he'd rather let "bodies pile high in their thousands" than order a new lockdown.
Mr Johnson insisted he did not make the comments, but admitted discussions on a lockdown last October were "very bitter" and "very difficult".
"Somebody here isn't telling the truth," Sir Keir hit back, reminding Mr Johnson of the ministerial code, which says "ministers who knowingly mislead Parliament will be expected to offer their resignation".
"I'll leave it there for now," he added.
Sir Keir's cryptic response appeared to suggest he knows further information on the subject would emerge - two witnesses have already told ITV News they would swear under oath to confirm Mr Johnson made the comments.
The Labour leader then moved on to the Downing Street flat, asking five questions about it, repeatedly pressing the prime minister on who initially paid for the refurbishment.
Who initially paid for the renovations?
Mr Johnson was able to bat away the first attack, accusing Sir Keir of misleading Parliament and insisting he had paid for the flat's refurbishment's "personally", adding he would make any further declarations if necessary.
The prime minister refused to directly answer Sir Keir's questions on who "initially" made payments for the flat, after it was exclusively revealed by ITV News Political Editor Robert Peston that costs were covered in the form of a loan from the Tory Party.
Sir Keir revised his question, and hit the prime minister with a multiple choice set of answers.
"Either the taxpayer paid the initial invoice, or it was the Conservative Party, or it was a private donor, or it was the prime minister."
"I'm making it easy for the prime minister," Sir Keir said, "it is now multiple choice - there are only four options, it should be easier than finding the chatty rat."
The Labour leader was making reference to a government inquiry which failed to find who leaked info to journalists about a lockdown last year.
Clearly frustrated by the question, Mr Johnson exclaimed: "I've given him the answer and the answer is I have covered the costs."
"I've conformed in full with the code of conduct," he said, adding: "I think people will find it absolutely bizarre that he is focusing on this issue."
His answer did not directly address the question of who made the "initial" payment for the flat, regardless of whether Mr Johnson was now paying for it himself.
Sir Keir said the public "scream at their televisions" every week at PMQs for Mr Johnson to "answer the question".
"The Prime Minister hasn't answered the question," Sir Keir said, "he knows he hasn't answered the question, he never answers the question."
Have any rules been broken about declaring who paid for renovations?
The Labour leader reminded Mr Johnson he is required to declare any benefits that relate to his political activities, including loans or credit arrangements, within 28 days.
He added: "He will also know any donation must be recorded in the register of ministers' interests and, under the law, any donation of over £500 to a political party must be registered and declared. So, the rules are very clear.
"The Electoral Commission now thinks there are reasonable grounds to suspect an offence or offences may have occurred. That's incredibly serious.
"Can the prime minister tell the House does he believe that any rules or laws have been broken in relation to the refurbishment of the Prime Minister's flat?"
Mr Johnson replied: "No, I don't. What I believe has been strained to breaking point is the credulity of the public."
The prime minister argued Sir Keir had failed to put "serious and sensible" questions to him about the pandemic or other issues, noting: "He goes on and on about wallpaper when I've told him umpteen times now, I paid for it."
'Dodgy contracts, jobs for their mates and cash for access - and who is at the heart of it?'
It was Sir Keir's final question which received the most furious response from the prime minister, in which he listed the principles meant to govern those in public office.
"Selflessness, integrity, objectivity, accountability, openness, honesty and leadership.
"Instead, what do we get from this Prime Minister and Conservative government?
"Dodgy contracts, jobs for their mates and cash for access - and who is at the heart of it? The Prime Minister, major sleaze sitting there."
A red-faced Mr Johnson fired back a shouty response, in which he attacked Labour and defended his own record in government.
"Week after week, the people of this country can see the difference between a Labour Party that twists and turns with the wind and thinks of nothing except playing political games, whereas this party gets on with delivering on the people's priorities."
Watch that Kevin Keegan moment: