The former president won his primary opponent by 20 points for his fourth straight victory.
As Trump congratulated him on his victory, he made no mention of Haley, who has pledged to stay in his race. Instead, he is targeting the November general election.
It will likely be a rematch with his successor in the White House.
After Saturday’s results came in, President Trump praised the “unity” of his party and said, “There has never been a spirit like this.” I have never seen the Republican Party so unified.”
It marked a shift from his response to last month’s primary in New Hampshire, where he raged against Ms Haley for “doing a speech like she won”.
Ms Haley, who once served as a popular two-term governor of South Carolina, congratulated her opponent on his victory in her speech.
She promised not to quit, however, saying the roughly 40% of the vote she received was “not some tiny group”.
“There are huge numbers of voters in our Republican primaries who are saying they want an alternative,” she said, emphasising that her continued campaign was not about her own political ambitions.
“I’m not giving up this fight when a majority of Americans disapprove of both Donald Trump and Joe Biden,” she added.
She has re-committed to staying in the race until at least Super Tuesday – 5 March – when voters in 16 states will cast their ballots on the same day.
“I’m a woman of my word,” the former UN ambassador said. “We’re headed to Michigan tomorrow, and we’re headed to the Super Tuesday states throughout all of next week.”
Flanked at his podium on the Columbia state fairgrounds by nearly two dozen allies, including most of the state’s political leaders, he told a raucous crowd: “This was a little sooner than we anticipated.”
Mr Trump certainly has much to boast about with this win. Exit polling conducted by the BBC’s US partner, CBS News, shows that the ex-president bested Ms Haley with both men and women, and among all age groups.
Lauding them for their support, Mr Trump, 77, reminded his audience: “We have a lot of work ahead of us.”
