Moore's defeat marks a major political blow to Trump, who endorsed the Alabama Republican and held a rally on his behalf. Although most national Republicans rushed to distance themselves from Moore in the aftermath of the allegations against him, Trump reaffirmed his support through tweets and public statements.
With all counties reporting, the Alabama Secretary of State reported Jones with 49.92 per cent of the vote, and Moore with 48.38 per cent of the vote.
The new Senator would be sworn in next year.
This is for the first time in a quarter century that a Democrat has won a Senate seat in a Republican stronghold of Alabama.
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Jones unexpected victory also narrows the Republican majority in the Senate to 51-49.
With 99 per cent of the votes counted, Moore, who fought allegations that he had molested or pursued relationships with teenage girls in the 1970s when he was in his 30s and an assistant district attorney, refused to concede.
"Democrats pull off an upset in Alabama," The New York Times said as it declared victory for Jones. The daily described as a rare Democratic victory in a staunchly Republican state.
The Washington Post described Jones' victory as a "shocking upset" in a solidly Republican state.
According to Time magazine, Jones' victory in Alabama, "was arguably aided by the rocky candidacy" of Moore.
With this victory, Jones a former US attorney, has become the first Democrat elected to the Senate from Alabama since 1992.
"Doug Jones will be an outstanding Senator who will represent Alabama well. He was a great candidate and will be an even better Senator," Senate Minority Leader Senator Chuck Schumer said.
"Congratulations to Doug Jones on a hard-fought victory," Trump tweeted.
"The write-in votes played a very big factor, but a win is a win," Trump said in his first reaction.
"The people of Alabama are great, and the Republicans will have another shot at this seat in a very short period of time. It never ends!" tweeted the US President.
However, Moore refused to concede, saying "Its not over".
His close aide indicated that a recount was still possible.
Indian-American Congresswoman Pramila Jayapal said Jones' win was a massive victory for the country.
Allegations of sexual misconduct against Moore drew national attention to the special election.
The claims against Moore came amid a wave of allegations of sexual misconduct against prominent figures that has led to the resignation of three politicians.