MPs Kenny MacAskill (East Lothian) and Neale Hanvey (Kirkcaldy and Cowdenbeath) were told to “get out now” by speaker of the House Lindsay Hoyle in furious scenes at the start of the session.
It comes as shouts of a Scottish independence referendum were heard in the chamber.
Mr MacAskill could be heard trying to raise a point of order and appeared to say “we need a referendum in the Prime Minister” before he was drowned out by other MPs.
Mr MacAskill refused to sit down and continued to speak, prompting Sir Lindsay to act.
Mr Hanvey then rose to his feet and could not be heard over the heckling from Tory MPs, before he was subsequently told to leave the chamber.
The Speaker said: “I will not tolerate such behaviour. If you want to go out, go out now.
“If you stand again, I will order you out. Make your mind up.”
Mr MacAskill rose to his feet again before Mr Hanvey also stood up and started speaking, but he could not be heard over the heckling from Tory MPs.
Sir Lindsay then named the pair, meaning they are suspended from the House.
He said: “Neale Hanvey, I’m now naming you and Kenny MacAskill to leave this chamber. Serjeant, deal with them.
“Out now, Serjeant-at-arms escort them out.”
In a press release from the Alba Party following the scenes, it states, “Kenny MacAskill and Neale Hanvey have today asserted that 'Scotland’s voice will be heard' in the face of a discredited Prime Minister’s continuing veto over a Section 30 order".
In an interview after he was thrown out, Kenny MacAskill, the former justice secretary told STV news: “This is a Prime Minister who is distorting parliamentary democracy, who is denying Scotland its legitimate right to a referendum and, at the same time, over half our people face, and Scotland is an energy rich country, fuel poverty.
“It’s time Scotland had the right to determine its own future rather than having a future determined by a handful of Tory MPs and then a handful of Tory members none of whom have been elected in Scotland.”
During PMQs, when asked about allowing Scotland to hold a second independence referendum by several SNP MPs, Mr Johnson said the SNP should look at “educational figures” instead of constantly bringing up the “constitutional issue”.
Ian Blackford said, “Scotland literally can’t afford the cost of living with Westminster” as he added: “Does the Prime Minister not get that the people of Scotland don’t just want rid of him, they want rid of the whole rotten Westminster system?”
The SNP Westminster leader also told the outgoing Prime Minister Boris Johnson the Conservative leadership is a "toxic race to the right", and the next Tory leader "will make Genghis Khan look like a moderate".
The PM said: “It’s thanks to our union that we were able to deliver the furlough scheme which helped the entire country and to make the massive transfers that boost the whole of the UK economy.
"The last thing the people of Scotland need now is more constitutional wrangling when we need to fix the economy.”