The Republican, whose campaign has been mired in scandal following allegations he sexually assaulted teenage girls in his 30s, lost by 1.5 per cent of the vote to Democratic challenger Doug Moore.
Although black voters had not been expected to turnout at the special election, caused by the appointment of former Alabama Senator Jeff Sessions as Attorney General, polls indicate they may have made up between 28 and 30 per cent of the vote.
The African American community makes up 27 per cent of the Alabama population, according to the 2016 census.
Media coverage prior to the election suggested overall black participation would be lower than exit polls suggest it was.
According to a preliminary breakdown by the Washington Post, black women in particular made up a decisive component of the vote.
African American women made up 18 per cent of the vote and approximately 97 per cent of their vote went to Mr Jones – compared with 65 per cent of white women (who made up 30 per cent of voters) opting for Mr Moore.
In contrast, the vote among black men made up just 12 per cent of the vote even though 92 per cent voted for Mr Jones.
Mr Moore, a former conservative judge, is best known for defying a Alabama Supreme Court ruling ordering him to remove a monument to the Ten Commandments outside a judicial building in the state capital Montgomery.
He was also a prominent member of the birther movement which claimed Barack Obama was not born in the US, and has courted controversy for his comments about gay people and Muslims.
But his campaign was thrown into chaos by several women saying they had been sexually assaulted by him in the past – two of his alleged victims said they had been 14 and 16 respectively at the time.
It is also alleged he had ties to pro-Confederate groups who celebrate the anniversary of Alabama’s secession from the United States over slavery during the US Civil War, CNN reported.
Mr Moore’s defeat is an embarrassment for Mr Trump who campaigned hard for the former judge despite allegations about his private life.
The President was quick to congratulate Mr Jones on Twitter even though he attacked him during the campaign as a “Pelosi/Schumer Liberal Democrat” who would “always vote against what we must do for our Country” and is “bad on Crime, Life, Border, Vets, Guns & Military [sic]”.
Mr Jones' victory is seen as a breakthrough for the Democrats as it is the first time they have won a Senate race in the deeply conservative state since 1992.
The Democrats have been on the backfoot since the Republicans swept into power in the House of Representatives as well as many statehouses and governor’s mansions in 2010.
Mr Jones' senate seat will have to defend his seat when it comes up for re-election in 2020, when Mr Sessions' original term was supposed to end.
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