Alabama Secretary of State John Merrill certified the election results at a meeting of the state canvassing board, which also includes Governor Kay Ivey and Attorney General Steve Marshall. Central time event, a Montgomery County circuit court judge had denied Moore's attempt to obtain a restraining order to stop the state's action.
Late Wednesday, hours before the Alabama State Canvassing Board was scheduled to meet Thursday to certify Jones' victory, Moore and his campaign filed a lawsuit alleging that voter fraud had tainted the election results and requesting that certification be delayed.
The allegations, first reported by the Post, may have been what cost Moore the election.
Alabama Secretary of State John Merrill certified the results of the December 12 special election and dismissed claims of voter fraud by the campaign of the defeated Republican candidate, Roy Moore.
In a statement following his victory's certification on Thursday, Jones said he is "looking forward to going to work for the people of Alabama in the new year".
Jones won 49.97 percent of the vote compared to Moore's 48.34 percent, a margin of almost 22,000 votes out of 1.35 million cast, officials said - a record for a special election.
Swearing-in ceremonies for Jones are set for January 3 when the Senate reconvenes from its winter break.
Moore appeared to be the favorite in the contest to fill the Senate seat held by Jeff Sessions, who is now Trump's attorney general.More news: The 2017 Holiday Season Could Be the Start of Retail's Big Comeback
Moore declined to concede defeat even after Trump urged him to do so.
As he launched his campaign, he said he saw an opening for a rare Democratic win against Moore, a polarizing figure in the state.
Jones, a former US attorney, claimed victory over Moore earlier this month, after various allegations of sexual misconduct plagued the Republican hopeful's campaign.
Moore claimed that "election fraud experts across the country have agreed that this was a fraudulent election", though an Alabama judge threw out Moore's lawsuit alleging voter fraud earlier Thursday afternoon.
"I have stood for the truth about God and the Constitution for the people of Alabama", he said.
The complaint also contained an affidavit from Moore "stating that he successfully completed a polygraph test confirming the representations of misconduct made against him during the campaign are completely false".
A day after the election, Merrill said it was "highly unlikely" that Jones, 63, would not be certified as the victor. He said Moore's complaint seemed to boil down to the belief that he should have won based on exit polling and that the high turnout, including by African-American voters, must indicate fraud.