Last week, between returning from their summer holidays and parliament's suspension, MPs passed a law to force Johnson to delay Brexit if he does not get a new deal by an European Union summit on October 17-18.
Last week a court in Edinburgh rejected the initial challenge, but this was overturned on Wednesday following an appeal.
The ruling added that all three First Division judges decided that the PM's advice to the British monarch was motivated by the improper goal of stymying Parliament and that it, and what has followed from it, is unlawful.
After the ruling, opposition politicians urged the government to scrap the suspension and recall lawmakers to Parliament.
While the Court of Session judges seemed to stop short of affirming that power, they said they can still rule on the advice's effect.
The decision by a three-judge panel on the Court of Session will not immediately force the government to allow lawmakers to reconvene - their suspension officially began on Tuesday, and they're not slated to meet again until October 14.
But there is no mechanism for MPs to be recalled between parliamentary sessions except at the request of the Prime Minister - and the government has said it will appeal the decision to the Supreme Court.
"The U.K. government needs to bring forward a strong domestic legislative agenda".
The action was brought before the court by a cross-party group of around 70 parliamentarians, who appealed against Lord Doherty's ruling.
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Others held up protest banners and shouted "Shame on you!" at ruling Conservative MPs. The government is looking for an escape route, says analyst Booth.
They stated the "improper objective of stymying Parliament" was behind Johnson's decision - not the stated motivation of introducing a new domestic legislative agenda.
"We are calling for parliament to be recalled immediately", said Scottish National Party lawmaker Joanna Cherry, who led the challenge, after Scotland's Court of Session ruled the prorogation should be annulled.
Labour's Brexit spokesman Keir Starmer welcomed the ruling, saying: "No one in their right mind believed Boris Johnson's reason for shutting down parliament".
HM (Queen Elizabeth II) acts on the advice of her prime minister.
Opponents said the real reason was to shut down debate and challenges to his Brexit plans.
"This was an egregious case of a clear failure to comply with generally accepted standards of behaviour of public authorities", concluded one judge, Philip Brodie, according to a summary of the court verdict. Ms Miller is appealing that decision in the Supreme Court.
Independent former Welsh Conservative MP Guto Bebb said Boris Johnson should resign if he has misled the Queen.
The judges had found in favour of a cross-party group of politicians, including a number of Welsh MPs. Downing Street said it was disappointed by the ruling and that the prorogation of Parliament had been "legal and necessary".
The court heard the prime minister was sent a note on 15 August asking if he wanted to prorogue parliament from mid-September. Parliament has already passed a law requiring the Prime Minister to seek an extension of the October 31 deadline if he hasn't reached a deal by October 19.