Third on the grid, Verstappen was second by the end of the pit straight after Ferrari's Kimi Raikkonen retired from second spot before the start with engine problems.
It took him only four laps to reel in pole-sitter Hamilton and from there the young Dutchman was never in any danger, taking a dominant victory on the day after his 20th birthday.
"I think in the beginning, straight away, the car felt good," said Verstappen.
"From there I could do my own race. The car was unbelievable, if I had to speed up I could. It was a very tough race and incredible to win."
Hamilton came second to extend his drivers' championship lead to 34 points over Ferrari's Sebastian Vettel.
Verstappen's Red Bull team-mate Daniel Ricciardo completed the podium at the Sepang International Circuit.
It was Verstappen's second career grand prix victory but only his second podium finish in a 2017 season which has seen him fail to finish seven of the 15 races.
The son of former Formula One driver Jos Verstappen was third at the Chinese Grand Prix back in April but has not appeared in the top three since because of crashes and retirements.
"I'm absolutely delighted for Max," Horner told reporters after the race.
"He's endured so much bad luck this season. He absolutely deserves this victory. He turned 20 yesterday and this is the best possible way to start that new decade," said Horner.
"He had pace all weekend. He did a great job yesterday and then to overtake Lewis, in the move that he made, was exemplary."
Ricciardo also won in Malaysia a year ago and Horner praised the Australian for overtaking the Mercedes of Valtteri Bottas to seize third before withstanding a fierce late challenge from Sebastian Vettel.
"Daniel was fantastic," said Horner, delighted with first and third for the team.
"He was unlucky starting on the damper side of the track but the pass he made to Valtteri, the way he defended against Vettel, was exceptional.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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