Malinin led all the way to take the title with a winning margin of 22.73 points over Japanese rival Yuma Kagiyama. Japan's Shun Sato won bronze after the free skating final.
"It's done. That's it," said an emotional Malinin after his performance in Prague.
"My expectation was to finish my free programme in one piece, and that has definitely happened.
"It was very awesome. I enjoyed every single part of it, and I'm so glad to be here."
The world championships in the Czech capital are taking place just a month after the Olympics, where Malinin had been the overwhelming favourite.
The undefeated star of skating for over two years had been leading after the short programme before crumbling under the pressure in the free skate to finish eighth.
Kazakhstan's Mikhail Shaidorov went on to win the Olympic gold ahead of Kagiyama and Sato, who took silver and bronze, respectively. Shaidorov skipped the world championships.
In his first competition since, Malinin took a 9.44-point lead from Thursday's short programme into the free skating final.
On Saturday, Malinin was more cautious than at the Olympic Games and simplified the technical aspects of his routine, notably swapping his trademark quadruple Axel for a triple Axel.
He also reduced the number of quadruple jumps from seven to five, nevertheless making an impressive comeback after the Olympic debacle, scoring 218.11 points for his free skate and 329.40 overall.
The 21-year-old Malinin became the first men's skater to win three titles since fellow American Nathan Chen from 2018 to 2021.
'Felt pushed and loved'
Kagiyama, 22, moved up from sixth after the short programme to achieve his fifth world medal and fourth in silver with 306.67 points.
Sato, 22, took a medal at worlds for the first time from fourth after France's Adam Siao Him Fa dropped from second to fifth after falling during his routine.
"I definitely felt pushed and loved, thank you so much, it was really challenging and really hard, but with you guys, I was able to make it through," said Malinin after receiving a prolonged ovation from the crowd, who continue to support him despite his Olympic disappointment.
"So much is happening in this sport, and of course, it wouldn't be possible without all of you for all the skaters, the support you give, motivation, and love and care that you give us; it really needs a lot of help to get where we are today."
The four-day world championships conclude later Saturday with Olympic ice dance champions Guillaume Cizeron and Laurence Fournier Beaudry on track for gold.
The French pair hold a comfortable lead of more than six points over Canadians Piper Gilles and Paul Poirier, the bronze medallists at the Milan-Cortina Olympics last month.
Britain's Lilah Fear and Lewis Gibson are third.
If he wins, Cizeron will clinch his sixth world title after five victories with his former partner Gabriella Papadakis between 2015 and 2022.
For Canadian-born Fournier Beaudry, it would be a first world medal.
