Doug Jones was confirmed as Alabama’s first Democratic senator in 25 years after state officials rejected a challenge to the shock result by his defeated Republican rival, Roy Moore.
Mr Jones, whose victory was ratified by John Merrill, Alabama’s secretary of state on Thursday afternoon, will be sworn in by Vice President Mike Pence on January 3 when the US Senate returns.
The election was upheld shortly after Montgomery Circuit Judge Johnny Hardwick denied Mr Moore’s request for a restraining order, which would have prevented Alabama’s canvassing board certifying the result.
It leaves the Republicans with a wafer-thin Senate majority of 51 to 49.
With John McCain, the Arizona GOP senator, being treated for cancer, the Republican majority is fragile especially with other Republicans, including Susan Collins of Maine, ready to break ranks with Mr Trump on issues such as the repeal of Obamacare.
Mr Moore, a Christian conservative, would normally have been expected to win comfortably in the election, caused by the appointment of sitting senator Jeff Sessions as Attorney General.
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Despite the support of Mr Trump – who had originally backed his rival Luther Strange for the Republican nomination – Mr Moore was defeated.
Mr Moore filed his challenge to the result late on Wednesday night, citing "irregularities in 20 precincts" in Jefferson County where, according to the latest estimate, just over 43 per cent of the population is African-American.
The alleged irregularities included claims that five busloads of black voters had been imported from Mobile, Alabama.
That proved to be unfounded, Mr Merrill said, as had allegations that three vanloads of Mexicans had been brought in to swell the Democrat total.
Mr Merrill said among the more than 100 complaints received was that 5,000 people had voted in an Alabama town with a population of 2,000. However, the investigation found that the town cited in the claim did not even exist.
The GOP candidate denied the allegations of sexual misconduct in the affidavit in which he said that he had taken a polygraph test.
Mr Moore has had little sympathy from fellow Republicans.
"I think it’s ridiculous," said Congressman Leonard Lance of New Jersey. "I am a strong Republican. I didn’t support Roy Moore. He should concede the election."