The ruling is a huge blow to Johnson’s authority, coming after a series of defeats in parliament that have curbed his plans to leave the European Union even if there is no divorce deal with Brussels.
The Speaker of the House of Commons, John Bercow, immediately announced that MPs would reconvene on Wednesday.
The Conservative leader, who is currently in New York, told British media he “strongly disagreed” with the decision but said he would respect it.
Johnson also renewed his call for an early election to end the stand-off with parliament.
He said it was “the obvious thing to do”.
Johnson had argued that shutting down parliament until October 14 was a routine move to allow his new government to set out a new legislative programme.
But critics accused him of trying to silence MPs.
Delivering the unanimous verdict of 11 judges, Supreme Court president Brenda Hale said “the decision to advise Her Majesty (Queen Elizabeth II) to prorogue was unlawful”.
She said this was “because it had the effect of frustrating or preventing the ability of parliament to carry out its constitutional functions”.
As a result, the suspension was “void and of no effect”, Hale said, adding: “Parliament has not been prorogued.”
The judge instantly became a social media sensation thanks to the large spider brooch she was wearing as she issued her strongly-worded condemnation of government policy.
Bercow subsequently announced that he would reconvene the Commons at 11.30 am (1030 GMT) on Wednesday morning, while the upper House of Lords said it would return the same day.
The judges “have vindicated the right and duty of parliament to meet at this crucial time to scrutinise the executive”, Bercow said.
A small group of protesters outside the court hailed the decision, with one, Gareth Daniels, telling AFP: “This is a great day for democracy.”
Jeremy Corbyn, the leader of the main opposition Labour party, led calls for the prime minister to step down.
“I invite Boris Johnson, in the historic words, to consider his position, and become the shortest serving prime minister there has ever been,” he told his party’s annual conference.
He brought forward his concluding speech to the meeting in Brighton, southern England, from Wednesday to Tuesday to allow him to return to parliament.
Some opposition MPs called for a confidence vote in Johnson, and Bercow indicated that he would allow time for this if a formal request were made.
The Supreme Court was ruling on two separate challenges, brought by more than 75 lawmakers and a team backed by former Conservative premier John Major.
“No prime minister must ever treat the monarch or parliament in this way again,” Major said after the verdict.
But Johnson is likely to resist any demands to step down, even if his Conservatives no longer have a majority in the 650-seat House of Commons.
Opinion polls suggest his battles with MPs over Brexit are actually making him more popular with voters.
Johnson only took office on July 24, but has endured a torrid few weeks in office as he battles a hostile parliament over Brexit.
Three years after the 2016 referendum, he insists Britain must leave the EU next month whatever the circumstances.
But lawmakers fear the disruptive impact of leaving without a deal, which the government itself has admitted could cause food and medicine shortages, and civil unrest.
In the week between returning from their summer holiday and prorogation on September 10, MPs passed a law aiming to stop “no deal”.
The law obliges Johnson to ask to delay Brexit by three months if he has not agreed a divorce deal by an EU summit on October 17 and 18.
Johnson said Tuesday that he hoped he can agree new exit terms to replace those struck by his predecessor Theresa May, which was rejected by MPs.
But EU leaders are not as hopeful, accusing London of failing to come up with serious alternatives to the current agreement. (AFP)