Following days of mixed messages from ministers, the Labour leader asked: “If somebody’s pinged by the NHS app, as millions will be over coming weeks, should they isolate yes or no?”
Responding virtually as he continues his self-isolation at his country retreat, Mr Johnson replied: “I think that everybody understands the inconvenience of being pinged, as he rightly says here I am, I wish I was with you in the Commons chamber today. I apologise to everybody in business up and down the land in all kinds of services, public sector or otherwise who are experiencing inconvenience.
“We will be switching, as the House knows, to a system based on contact testing rather than contact isolation, but until then I just must remind everybody that isolation is a vital tool of our defence against the disease.”
He added: “Everybody should get a jab.”
Sir Keir claimed the country was “heading for a summer of chaos” as he highlighted the one million children out of school last week and the "huge number" of businesses closing due to staff isolating.
Speaking at PMQs, he highlighted confusion over the isolation exemption list before adding: "I know the Prime Minister likes to govern by three-word slogans, I think 'on the hoof' might work pretty well."
Mr Johnson described Sir Keir's questions as "feeble stuff" and said: "He wants to keep this country, as far as I understand his position, in lockdown."
Confusion then emerged in the chamber as Speaker Sir Lindsay Hoyle said he was struggling to hear the Prime Minister, with Mr Johnson repeatedly saying: "Do you want me to have another go? Can you hear me? Do you want me to give that answer again?"
On self-isolation rules, Sir Keir said: "The Government's all over the place on this."
He said: "Yesterday his business minister said the app was an advisory tool only, another Government minister and, I kid you not, said yesterday the app is just to allow you to make informed decisions. What on earth does that mean?"
He added: "Of course the Prime Minister and the Chancellor spent the weekend trying to dodge isolation altogether. The British people are trying to follow the rules, how can they when his ministers keep making them up as they go along?
Mr Johnson replied: "No... isolation is a very important part of our armoury against Covid. We're going forward, as everybody knows, to a new system on August 16 based on testing but in the meantime when you're advised to isolate to protect others and to protect your family against the spread of the disease then you should do so."
He added: "And of course even more important than the isolation campaign is of course the vaccination campaign. Three million people of the 18-30 group have still to get one."
Sir Keir went on to highlight confusion and changes of policy over isolation exemptions and Covid vaccine passports, adding: "When it comes to creating confusion, the Prime Minister is a super-spreader.
"Why is it OK to go to a nightclub for the next six weeks without proof of a vaccine or test, and then from September it will only be OK to get into a nightclub if you've got a vaccine ID card?"
The Prime Minister accused Sir Keir of trying to "score cheap political points" and noted: "Everybody can see we have to wait until the end of September, by which time it is only fair to the younger generation, when they will all have got the two jabs, before we consider something like asking people to be doubled jabbed before they can go into a nightclub.
"That's blindingly obvious to everyone, it's common sense."