Merrill said the allegations of voting irregularities by Moore's team had been thoroughly investigated and found to be baseless, while a judge threw out a suit seeking to delay the results certification.
Conspiracy theories have spread in online conservative groups since the election, alleging without evidence that black voters were bussed in from other states to vote for Mr Jones.
The Alabama State Canvassing Board, which includes Gov. Kay Ivey, Secretary of State John Merrill and Attorney General Steve Marshall, signed the certification to officially confirm Jones' stunning victory over embattled Republican Roy Moore. Previously, Merrill has said it is "highly unlikely" that Jones would not be certified as the victor of the election.
"Doug Jones will be certified today at 2 p.m. eastern time, 1 p.m. central time", Alabama Secretary of State John Merrill told CNN's New Day this morning.
In his election complaint, Moore stated that he took a polygraph test over the sexual misconduct allegations made against him by Leigh Corfman, Beverly Nelson and Tina Johnson.
He unexpectedly lost to Jones by about 20,000 votes in the special election to fill the Senate seat vacated by Jeff Sessions, who is now US attorney general.
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 win came after Moore, best known for stands against gay marriage and the public display of the Ten Commandments, was dogged by accusations of sexual misconduct involving teenage girls that occurred decades ago.
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If the election is prematurely certified, Mr. Moore's lawyers wrote, he will "suffer irreparable harm" and be "denied his full right as a candidate to a fair election".
Mr Jones will be sworn in on January 3 and is the first Alabama Democrat elected to the Senate in 25 years.
Unusual lost the Republican primary to former Alabama Supreme Court Justice Roy Moore.
Jones defeated Moore by about 20,000 votes. He takes over the seat previously held by Attorney General Jeff Sessions.
Rick Hasen, an election law expert and professor at the University of California, Irvine, said Moore's complaint did not raise the sort of issues that lead courts to overturn an election. "To God be the glory", Moore said in a statement sent out more than two weeks after he lost the special election as a Republican in the deep-red state.
Photo Roy Moore addressing supporters at a rally in Midland City, Ala., a day before the December 12 Senate election. The complaint also noted the higher-than-expected turnout in the race, particularly in Jefferson County.