With 42%of the vote in, Moore, the former chief justice of the Alabama supreme court was ahead of appointed incumbent Luther Strange by a margin of 57 to 43%, in the Republican Senate runoff on Tuesday night.
Muddying the waters was the fact that many of Trump's own former aides and surrogates - and even one of his current cabinet secretaries, Ben Carson at HUD - lined up against him to support Moore. Can Trump push an "establishment" candidate like Luther Strange past a "Breitbart" wing candidate like Roy Moore? Finish the job - vote today for "Big Luther".
Former White House chief strategist Steve Bannon threw his support behind Moore.
Stewart said he is not convinced Trump's endorsement of unusual swayed voters.
Though voters rejected his candidate of choice, President Trump remains popular in Alabama, which he won by 28 points previous year.
In a state as deeply conservative as Alabama - Republicans outnumber Democrats in the state about five to three - the victory means Moore will nearly certainly be Alabama's next senator.
In an upset likely to rock the GOP establishment, Moore clinched victory over Sen. That can mean you hate your black neighbors, or you're a social justice warrior who thinks the word "becky" is just as bad as saying "nigger".
"If Alabamians send Moore to the U.S. Senate, they will be sending a message to the swamp in Washington, D.C., that they do not support Senate Majority Leader Mitch McConnell and others' efforts to dilute the agenda that President Trump campaigned on", he wrote.
If you know Alabama politics, you know Roy Moore has been in the forefront for nearly two decades now. A populist who believes in the supremacy of God's law over man, Moore has addressed white supremacy groups, doesn't believe Muslims can serve in Congress, and was twice reprimanded for defying federal court orders.
Alabama has not elected a Democrat to the Senate in a quarter of a century, so Mr Moore will be expected to beat his Democratic rival Doug Jones when they face off in a vote on 12 December.
In addition to the national backdrop, a number of state factors are at play in the race to fill the remainder of Attorney General Jeff Sessions' Senate term.
Despite Strange's loss, Trump remains popular in the state.
In the 24-hours before Tuesday's vote, he urged voters to turn out for odd. I'm a Trump voter.
"It was sort of a 'you scratch my back and I'll scratch yours, '" said R.L. Barber, 77, a Moore supporter from Birmingham.
A steady flow of voters at the Dean Rd. polling location in Auburn Tuesday.
Merlene Bohannon, a widow with three grown children, said she had planned to vote for unusual until seeing Bannon stump for Moore on Fox News on Monday night.
"They tried to destroy Donald Trump; the same gang that is going after Roy Moore is the same gang that went after Donald Trump", Bannon said.