A scuffle broke out in the Commons and signs bearing the word "silenced" were held by some MPs, as Parliament was suspended for five weeks.
The prorogation came just hours after Boris Johnson’s second attempt to trigger an early general election failed when his motion did not secure the required support of two-thirds of MPs.
In order for the suspension of Parliament to begin, the Speaker was requested to lead MPs to the Lords, but as this happened, Labour's Lloyd Russell-Moyle appeared to try to hold on to John Bercow and appeared to be forcibly removed.
Shouts of "shame on you" could be heard as Government MPs left the Commons to head to the House of Lords for the prorogation ceremony.
The scenes came amid a tense day in the Commons which saw the Prime Minister defeated for the sixth time in six days.
Mr Johnson said he wanted to head to the polls next month to break the political deadlock, as he accused opposition parties of making "outrageous excuses" to delay.
But Labour and other opposition MPs refused to back the bid – which needed a two-thirds majority in the Commons – while the risk of a no-deal remained.
MPs voted 293 to 46, short of the 434 needed - marking the new PM’s sixth Commons defeat.
Soon after the election vote, the prorogation was passed in the early hours of Tuesday, making a general election extremely unlikely until at least mid-November.
The move to prorogue sparked outrage among many MPs, with one Labour politician recalling what happened to King Charles I when he prorogued Parliament.
Barry Gardiner said: "We are in extraordinary times, a five week prorogation - 370 odd years ago we executed a king for proroguing Parliament in this way."
"It's one law for him and another for everybody else."
After his defeat at the hands of MPs, the Prime Minister said Jeremy Corbyn had become the first leader of the opposition in the country's history to "show his confidence" in the Government "by declining the opportunity to have an election with a view to removing the Government".
But amid stormy scenes in the chamber Mr Corbyn said he would not let his party walk into "traps laid by this Prime Minister".
"This Government is only interested in shutting down Parliament to avoid any scrutiny," the Labour leader said.
The PM insisted he would not ask for another Brexit delay, despite royal assent being given to legislation requiring an extension to the UK's EU membership unless a divorce deal is approved or Parliament agrees to leaving the EU without one by October 19.
Mr Johnson said: "It's plain from the turbulent reaction of the benches opposite that they simply want another delay and I will not have that.
"I must warn members that their behaviour in thwarting the will of the people is undermining respect for this House in the country.
"If honourable members want a delay, the only proper way to do it is to ask permission from our masters the people, from our masters the voters."
He said Mr Corbyn had previously said he would back an election if legislation to prevent the Government from forcing through a no-deal Brexit on October 31 became law.
The PM added: "The surrender act has now passed, it's gained royal assent, he's done his level best to wreck this country's chances of a successful negotiation.
"By his own logic, he must now back an election."
Mr Johnson - who on Tuesday was expected to continue campaigning for the election he is yet to successfully call - said an election is the only way to break the deadlock in the Commons.
He continued: "Throughout the weekend (Mr Corbyn's) cronies, together with those of other opposition parties, have been trying to disguise their preposterous cowardice by coming up with ever more outrageous excuses for delaying an election until the end of October or perhaps November or when hell freezes over."
Following the defeat, Mr Johnson said the Government would "press on with negotiating a deal while preparing to leave without one" ahead of the European Council summit on October 17.
The Prime Minister said: "No matter how many devices this Parliament invents to tie my hands I will try to get an agreement in the national interest.
"This Government will not allow Brexit to be delayed any further. While the opposition run, they cannot hide forever."
During a noisy Commons debate, Mr Corbyn said the Prime Minister was trying to avoid scrutiny.
He said: "This Government is only interested in shutting down Parliament to avoid any scrutiny.
"His obfuscations and evasions are being rumbled - both at home and abroad - and that is why he doesn't answer questions and he is so keen to avoid scrutiny.
"Tonight he will attempt to prorogue Parliament for one of the longest prorogations there has ever been - shutting down Parliament, shutting down democracy, avoiding questions, taking this country over a cliff of a no-deal exit with all the damage that will do to many of the poorest and most vulnerable communities in our society."
Earlier on Monday evening, MPs backed a motion to force the government to publish communications linked to prorogation and documents connected to no-deal Brexit planning.
It was put forward by axed Tory MP and former attorney general Dominic Grieve and demands that all Government all international correspondence, including emails, WhatsApp and Facebook messages, about the temporary suspension of Parliament and Operation Yellowhammer documents since July 23 be released.
The motion was approved by 311 votes to 302, a majority of nine.
However a Downing Street source told ITV News Political Editor Robert Peston that "under no circumstances will Number 10 staff comply with Grieve's demands regardless of any votes in Parliament".
It came after John Bercow announced he will stand down as Commons Speaker at the end of next month, unless an election is called before then.
In an impassioned speech to the Commons, Mr Bercow – who has been Speaker for 10 years – also said he would step down as an MP.
Tuesday will see Mr Johnson continuing to campaign for an election when he visits a primary school in London to mark the launch of an education drive which could see up to 30 new free schools established.