Ian Blackford refused to sit down when ordered to by John Bercow having asked for the Commons to sit in private.
This was in protest at the government's handling of debate and votes on the EU Withdrawal Bill.
And it brought PMQs to a temporary halt as the Speaker consulted his officials on what to do next.
Mr Bercow said MPs could vote on his request for a private sitting at the end of PMQs - but when Mr Blackford refused to sit back down he was suspended for the rest of the day's sitting
His fellow SNP MPs followed him out of the chamber.
The episode took place during the weekly PMQs session after Mr Blackford said it was a "democratic outrage" that MPs had not been given enough time to debate measures he described as a "power grab" by Westminster from Scotland.
He added: "Under the circumstances, given the disrespect that's shown, I have got no option but to ask that this House now sits in private."
Mr Bercow said it was better for a vote on his request to take place at the end of the session - but the SNP MP did not agree, rejecting repeated orders from the Speaker to resume his seat.
The next MP to be called for a question was Conservative MP Luke Hall, who joked: "With the amount of people leaving, it feels like one of my after-dinner speeches."
Well well! High drama as the SNP Leader Ian Blackford sought revenge for yesterday's manoeuvrings, which limited debate on devolution amendments to the EU (Withdrawal) Bill to 20 minutes. He sought to move that the House sat in private, a motion which is normally voted on immediately.
It would have broken up PMQs, and the Speaker said he would not take the vote until afterwards. Mr Blackford kept up his protests and was eventually ordered out - to be followed by his entire contingent of MPs.
They didn't go far, because moments later he was giving an interview to the BBC in Central Lobby, a few yards outside the Chamber.
There is no doubt the SNP are very angry about what happened yesterday - and they have never been shy of staging a bit of performance art to highlight what they see as the corrupt, archaic ways of Westminster. I suspect this is Act One, and more drama lies ahead
The Brexit bill says that the "vast majority" of the 158 areas where policy in devolved areas is currently decided in Brussels will go directly to the Scottish and Welsh parliaments after Brexit.
But it has also named 24 areas where it wants to retain power temporarily in the wake of Britain's exit from the EU, including in areas such as agriculture, fisheries, food labelling and public procurement.
It says the "temporary restriction" on the devolved governments using some of the powers returning from the EU is needed "to help ensure an orderly departure from EU law" and allow the same rule and regulations to remain in place across the whole of the UK.
But the Scottish government argues that it would leave Holyrood unable to pass laws in some devolved areas for up to seven years.
It has produced its own alternative Brexit legislation, which was passed by MSPs in March but is currently subject to a legal challenge by the UK government.