Premier Doug Ford had argued the move would improve decision-making and save $25 million.
The notwithstanding clause allows a provincial government to suspend a part of the Canadian Charter of Rights and Freedoms for a period of up to five years.
This will be the first time that the clause will be used in Ontario's history.
This is a breaking news update. Belobaba called Bill 5 "profoundly unfair" and found that nothing the government's lawyers had presented could reasonably explain why the 47-ward election for a city of almost 3 million people needed to be cancelled by legislative fiat.
Superior Court Justice Edward Belobaba said in his decision that Ontario Premier Doug Ford's government "clearly crossed the line" with Bill 5, the Better Local Government Act, which would have cut the number of municipal seats from 47 to 25.
Horwath thanked Belobaba for his work and all those who gave their time and expertise to the court battle against Ford's move to meddle in Toronto's municipal elections.
"(Reducing and streamlining council) will fix this dysfunctional government. "The province has exclusive responsibility over municipalities", said Ford in announcing his government's action.
"I believe the judge's decision is deeply concerning and the result is unacceptable to the people of Ontario", Ford said.
Chris Moise, who is running for council, said he is proud to have stood up for the city and win.
Ontario Premier Doug Ford is pictured at a meeting of economists from major Canadian banks on August 30, 2018.
But that mistake, quickly seized upon by his opponents once they had recovered from the shock and horror of Ford's main announcement, doesn't make him unique.
"But", he added, "this was an unprecedented situation because the change in the number of wards was happening in the middle of an election". "That's not fair to anyone, and this is not a game", he said.
Why didn't he campaign on it in the June provincial election? Tory told reporters on Tuesday.
Bill 5, the Better Local Government Act, was rushed through the Ontario Legislature and passed August 14, even though campaigning for Toronto's municipal election began May 1.
Now, Tory said, he wants answers from the province about why it tried to cut the size of council to begin with.
Ford said he'd be recalling the legislature this week to introduce legislation that will invoke the notwithstanding clause.
Jennifer McKelvie, a candidate running east of Toronto, was knocking on doors Tuesday outside of what would have been the ward she meant to run in for the 47-seat system.
Mayor John Tory speaks to a member of the public after holding a media scrum in front of city hall in Toronto, on September 11, 2018. "It is inexcusable that the Ford government targeted only the city of Toronto for these dramatic changes", Fletcher said.
Many current and prospective city councillors also applauded the verdict.
Coun. Mike Layton said he hopes the ruling serves as a "lesson" to Doug Ford and his government.
"The Ford government has acted in a reckless and capricious manner and it must stop interfering in democratic elections".
He also tut-tutted about the province's lack of consultation, though he noted there's no duty on legislators to consult before passing a bill. "And we won", he tweeted. "For not only councillors, but frankly residents of our city to understand what the new rules are, what the new timelines are, what the new wards are". "Nominations under the 25-ward model were closed following the Superior Court ruling". "Today, we celebrate!", said councillor Joe Mihevc on Twitter on Monday.
But, if Ford gets his way by forcing a reversal, it's not clear if there will be an opportunity for those who have not yet signed up to register in the 25-ward race.
"We encourage the Ford government to appeal this decision immediately".
And besides, Ford et al were elected and judges aren't.
"The issue here is whether he was really drawing in elements from another Charter right, which is the Section 3 right to vote", she wrote.