Gov. Cuomo fought off a challenge from the left and captured the Democratic nomination for governor Thursday as New Yorkers rejected progressive challenger Cynthia Nixon in the party’s state primary.

With 99 percent of the vote counted, Cuomo was crushing Nixon 66 percent to 34 percent, nearly the same margin he beat Zephyr Teachout by in 2014.

Cuomo performed well across the state and won all five boroughs in the Big Apple.

A minute after voting ended at 9 p.m., Nixon released a statement essentially conceding the race and declaring that since polls showed Cuomo up by as much as 41 points, a narrower margin of victory could be seen as “a major embarrassment and significant underperformance for the two-term incumbent.”

Later, addressing a cheering throng at Cafe Omar in Flatbush, Brooklyn, the former “Sex and the City” star said her candidacy had pushed Cuomo to the left.

“We have fundamentally changed the political landscape in this state. And we have changed what is expected of a Democratic candidate running in New York and what we can demand from our elected leaders,” Nixon said.

“People are struggling just to survive here, and we need real substantive policies that address racial, gender and economic inequality in New York state . . . This campaign forced the governor to make concrete commitments that will change the lives of people across the state.”

The governor’s running mate, Lt. Gov. Kathy Hochul, overpowered an early lead by her progressive rival, Brooklyn Councilman Jumaane Williams, to eke out a 53 to 47 percent victory.

But Williams warned that his campaign sent a message that progressives are on the march.

“We will hold Democrats responsible for what they say,” he said. “And, Andrew Cuomo, we see you now, you can’t hide. We will hold you accountable, too.”

The third member of Cuomo’s team, attorney-general candidate Letitia James, also won.

Former Council Speaker Christine Quinn, a Cuomo backer, celebrated the governor’s win at the Democratic Party’s celebration at the Ainsworth restaurant on East 33rd Street.

“I love an early result when the person I’m supporting is the winner. There’s still a lot of polls coming in, so I’m excited to see what our final number is — how high it is,” she said.

John Samuelsen, president of the Transport Workers Union, also hailed the win.

“It’s a victory for trade-union workers in New York state and blue-collar workers in New York state,” he said. “The governor has demonstrated himself over the last several years to be an extremely pro-worker, pro-trade union governor . . . and we couldn’t be more ecstatic about his victory.”

The primary results could be seen around the nation as a sign of how the party’s insurgent left wing will fare in its efforts to oust establishment incumbents.

Nixon had hammered Cuomo for failing to address Gotham’s decrepit subways and for not following through on pledges to stamp out Albany’s ethics lapses.

The former actress said she represented a wave of progressives eager to take a greater role in American politics.

Cuomo, meanwhile, touted liberal accomplishments such as gun control, free public college tuition and a higher minimum wage.

He spent millions of dollars on ads and tried to make the race about President Trump, arguing he was the best qualified to push back against the White House.

Polls had showed Cuomo with a commanding lead throughout.

Nixon often invoked Democratic Socialist Alexandria Ocasio-Cortez’s primary victory over longtime Congressman and Queens party boss Joe Crowley as evidence that underdog challengers can defy the odds.

While he seldom mentioned her by name, Cuomo took Nixon seriously as a political threat.

He moved to the left on issues such as legalizing marijuana, returning voting rights to former inmates and addressing conditions in the city’s public housing.

The race was marked by bitter attacks, with Nixon calling Cuomo a “bully” and liar and the governor’s campaign dismissing her as “unhinged.”

Cuomo racked up endorsements from a wide assortment of figures, including Joe Biden, Hillary Clinton and Nicki Minaj.

Nixon hoped recent missteps by Cuomo and his campaign would come back to bite him.

Cuomo was mocked for saying America “was never that great” while criticizing Trump’s “Make America Great Again” slogan.

He also claimed to have no knowledge of a Democratic Party mailer that all but called Nixon, a practicing Jew, an anti-Semite.

After voting Thursday, Cuomo said he ran a “fully positive” campaign — a statement a top Nixon aide mocked as a fantasy.

“Governor Cuomo was bitter and divisive until the very end,” senior campaign strategist Rebecca Katz said in a statement.

Additional reporting by Nolan Hicks, Carl Campanile and AP