Sir Keir was bundled into a police car for protection near Parliament as he faced allegations of “protecting paedophiles” from protesters shouting about Savile.
Making a statement to the Commons on Tuesday, Sir Lindsay Hoyle criticised the “disgraceful behaviour” directed at the Labour leader and shadow foreign secretary David Lammy.
He told MPs: “I deplore the fact that members of this House were subjected to intimidating and threatening behaviour while simply doing their jobs.
“I know the whole House will join me in saying that we stand with our colleagues in condemning the behaviour they and the police experienced.
“While I do not comment in detail on security matters on the floor of the chamber, steps must be in place to keep passholders secure as they enter and leave the parliamentary estate.
“I have requested a situation report from the Metropolitan Police via our security team on how this incident occurred.”
Sir Lindsay said he understood arrests had been made following the incident, adding: “I know it has been reported that some abuse was directed at the leader of the Opposition yesterday related to claims made by the Prime Minister in this chamber.
“But regardless of yesterday’s incident, I made it clear last week that while the Prime Minister’s words were not disorderly, they were inappropriate.
“As I said then, these sorts of comments only inflame opinions and generate disregard for the House and it is not acceptable.
“Our words have consequences and we should always be mindful of the fact.”
Lib Dem MP Alistair Carmichael demanded Mr Johnson withdraw his “shameful slur”.
He said: “When the Leader of the Opposition is being attacked by a mob citing the Prime Minister’s words, there has to be a reckoning.
“This must be a moment of change for Conservative MPs. It has festered long enough – we risk long-term damage to our political culture unless there is a meaningful break from the Prime Minister’s toxicity.
"He must apologise, he must go – and Tory MPs will be complicit until they force him out.”
The sister of murdered MP Jo Cox has said she found the scenes of Sir Keir being rescued from a mob “really upsetting”.
Kim Leadbeater said: “Words and that culture filters down to other people and it really concerns me that we have got a Prime Minister who seems to be stoking the anger that people feel in the country at the moment and that can have real repercussions for society.”
Downing Street insisted Mr Johnson would not apologise for his controversial attack and claimed his language was misunderstood.
The Prime Minister’s official spokesman acknowledged his original words last week in the Commons were “capable of being misconstrued”, which was why he subsequently issued a “clarification”.
He said: “The Prime Minister clarified his remarks last week to make clear he was not suggesting Keir Starmer was individually responsible for the Savile decision.
“I think the Prime Minister was making a political point about taking responsibility for organisations as a whole.”