The former Scottish First Minister was told to “sit down” repeatedly by Mr Hoyle and other members of the House after he snapped against the treatment of his SNP colleague Joanna Cherry.
As the clock approached midnight, Mr Hoyle, who was chairing the debate, called Ms Cherry to speak.
When she made it clear she would “take as much time” as she needed to make her points, the Deputy Speaker swiftly said her speech had come to an end.
Alex Salmond reacted furiously at a Brexit debate
You cannot reinterpret the wishes of an honourable member who is on her feet
Shown on Parliament TV, a visibly angry Mr Salmond said: “It is quite clear that the honourable lady had not resumed her seat, Sir.
“Being in the Chair accords you many privileges, but you cannot reinterpret the wishes of an honourable member who is on her feet.”
Hitting back, Mr Hoyle said he had the right to make such decisions and he did not expect to be taken advantage of over timings.
Refusing to sit down, Mr Salmond continued his point.
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Continued cooperation with the EU to tackle terrorism and international crime.
Another SNP MP, Ian Blackford also rose to his feet to describe the party's “frustration” that only two of their representatives had been called in the debate, which was about the role of devolved administrations in the Brexit negotiations.
Mr Hoyle said: “Tempers are running quite high. We need to just calm it down. In fairness I’ve been very generous in coming into the chair.”
Mr Salmond, MP for Gordon, has warned the UK government that the SNP will challenge it “tooth and nail” on Brexit.
He said: “The SNP will fight tooth and nail to blunt the axe of a hard Brexit falling again this week.”