MONTGOMERY, Ala. — Firebrand jurist Roy Moore won the Alabama Republican primary runoff for U.S. Senate on Tuesday, defeating an appointed incumbent backed by President Donald Trump and allies of Sen. Mitch McConnell.

In an upset likely to rock the GOP establishment, Mr. Moore clinched victory over Sen. Luther Strange to take the GOP nomination for the seat previously held by Attorney General Jeff Sessions.

Mr. Moore will face Democrat Doug Jones in a Dec. 12 special election to serve out Mr. Sessions’ term, which runs through the 2020 election cycle. He will be heavily favored in conservative Alabama.

Mr. Trump quickly tweeted out his support for Mr. Moore, writing “Congratulations to Roy Moore on his Republican Primary win in Alabama. Luther Strange started way back & ran a good race. Roy, WIN in Nov!”

Mr. Strange’s campaign had emphasized his endorsement from Mr. Trump, urging voters to get to the polls before they closed at 7 p.m. local time in a Tuesday email message saying “President Donald Trump needs you NOW!”

But the race wasn’t a direct referendum on Mr. Trump, as Mr. Moore also emphasized his pro-Trump stance. At the Moore victory announcement, at least one person standing onstage next to Mr. Moore was wearing the iconic red “Make America Great Again” cap.

He also won the support of former White House strategist Steve Bannon, arguing he’s a better fit for the “populist, nationalist, conservative movement.” Mr. Bannon spoke at a Moore rally Monday night and attended Mr. Moore’s election-night party in Montgomery.

The crowd at Mr. Moore’s election party broke into loud applause as media outlets called the race. Mr. Bannon declared the Moore win a victory for Mr. Trump, despite the president’s support for Mr. Strange.

“Who is sovereign, the people or the money? Alabama answered today — the people,” Mr. Bannon said.

A super PAC aligned with Mr. McConnell had pumped millions of dollars into the Alabama race on behalf of Mr. Strange, a point Mr. Moore constantly made arguing the election was an opportunity to send a message to the “elite Washington establishment” that he said was trying to influence the race.

The Senate Leadership Fund, a group with ties to Mr. McConnell, had spent an estimated $9 million trying to secure the nomination for Mr. Strange.

Senate Leadership Fund President and CEO Steven Law said Tuesday that Mr. Moore won the nomination “fair and square” and said Mr. Moore “has our support, as it is vital that we keep this seat in Republican hands.”

Mr. Moore led Mr. Strange by about 25,000 votes in the crowded August primary, which went to a runoff between the two because neither topped 50 percent in the voting.

Mr. Moore was twice elected chief justice of the Alabama Supreme Court and twice removed from those duties.

In 2003, he was removed from office for disobeying a federal judge’s order to remove a Ten Commandments monument from the state courthouse lobby. Last year, he was permanently suspended after a disciplinary panel ruled he had urged probate judges to defy federal court decisions on gay marriage and deny wedding licenses to same-sex couples.

Mr. Strange told his supporters that “we wish [Mr. Moore] well going forward.” But he quickly shifted to his own bewilderment at the race he just finished.

“We’re dealing with a political environment that I’ve never had any experience with,” he said.

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