Opposition MPs alleged some Tories had been bullied and manhandled into voting with the government on fracking.
A minister denied the claim, but many Tory MPs ended the day feeling angry and let down by their own party.
One Conservative MP Charles Walker said the situation was a "shambles".
Visibly furious, he told the BBC: "I've really not seen anything like tonight", adding that there was "no coming back" for the government.
Later he added: "I expect the prime minister to resign very soon because she's not up to her job."
Downing Street had started Wednesday believing the prime minister was on a more solid footing after the appointment of Jeremy Hunt as chancellor - and his decision to reverse much of Ms Truss's mini-Budget - appeared to have calmed the markets.
She also survived Prime Minister's Questions - the weekly question session with MPs - relatively unscathed.
However, things began to unravel for Ms Truss shortly after.
The prime minister was forced to hastily cancel a visit to an electronics manufacturer in order to have a meeting with her then-Home Secretary Suella Braverman after she broke government data rules.
The BBC has been told Ms Braverman breached the ministerial code by sending a government document to someone not authorised to receive it.
In her resignation letter, Ms Braverman acknowledged there had been "a technical infringement of the rules", adding: "I have made a mistake; I accept responsibility: I resign."
However, she also took an angry swipe at the government by accusing it of breaking "key pledges" and failing to reduce immigration numbers.
Her departure makes Ms Braverman the shortest-serving home secretary since World War II - and comes less than a week after the resignation of Kwasi Kwarteng as chancellor.
Grant Shapps - who Ms Truss had sacked as Transport Secretary six weeks ago - became the new home secretary.
Shortly after Mr Shapps arrived at the Home Office to start his new job, chaotic scenes began to play out in the Commons, where MPs were voting on fracking.
Labour had tabled a vote which, if passed, would give MPs a say on the government's plans to bring back fracking.
Many Conservatives have spoken out against bringing back fracking but they were told that the vote was being regarded as a vote of confidence in the prime minister and government.
This meant that if they did not side with the government they could be kicked out of the parliamentary party.
Labour MP Chris Bryant claimed some Conservative MPs had been physically manhandled in the voting lobbies to make sure they supported the government.
And a Labour shadow minister, Anna McMorrin, wrote on Twitter that she witnessed one Conservative MP "in tears being manhandled" in the voting lobby in Parliament.
However, Conservative, Alex Stafford, hit back at claims he had been manhandled saying there had simply been a "frank and robust conversation" about his opposition to fracking.
Business Secretary Jacob Rees-Mogg also said he wouldn't characterise the events as bullying.
The fallout from the vote led to speculation that Chief Whip Wendy Morton - who is in charge of party discipline - and her deputy Craig Whittaker had left their posts.
Rumours were fuelled by government silence on the issue and at one point, Mr Rees-Mogg told Sky News he was "not entirely clear" about the situation.
However, after a few hours, it emerged that both Ms Morton and Mr Whittaker were remaining in post.
Earlier in the day, it was revealed that one of Ms Truss's most senior advisers has been suspended amid a formal investigation by the Propriety and Ethics Team, which is responsible for standards across government.
It followed some anger from Conservative backbench MPs about briefings to newspapers from No 10 sources over the weekend - including disparaging remarks about former Health Secretary Sajid Javid.
Former Brexit minister Lord David Frost - once an ally of Ms Truss - has written a piece in the Daily Telegraph calling on the prime minister to go.
He argued that she was "implementing neither the programme Liz Truss originally advocated nor the 2019 manifesto", adding: "There is no shred of a mandate for this. It's only happening because the Truss government messed things up more badly than anyone could have imagined.. something has to give".
WATCH: 'That looked like bullying to me' - Chris Bryant
WATCH: 'I've had enough of talentless people' - Charles Walker