Verstappen grabbed the lead from then race leader Hamilton on lap 4.
"The auto was unbelievable, if I had to speed up I could".
Hamilton had endured a torrid Friday as his Mercedes took a dislike to an aerodynamic upgrade package. "They (Red Bull) just had the upper hand on us today". "I feel positive, the debrief was one of the best debriefs we have had".
The race did throw challenges in the way of Vettel, who rose to the occasion and put in a good effort to move from dead last (20th position) to 13th on the first lap.
It had threatened to be a shocking day for Ferrari after a turbo issue prevented Kimi Raikkonen from starting the race, but Vettel's recovery will provide some consolation to the Scuderia.
But it's Hamilton winning the war. How can we fix our issues? We were running less downforce than the others - we don't have the T wing or the Carry wing on here, and we found a very good setup and the drivers have delivered their bit as well.
Vettel, who led the championship until just a month ago, now has only five races left to overhaul Hamilton's big lead, starting next week in Japan.
"I am still optimistic, because we know that we have a quick auto", said Vettel.
"We can look after our tyres quite well, so hopefully that's a benefit maybe for some upcoming races but we have to wait and see".
The championship leader scorched the 5.5-kilometre long Sepang track in one minute 30.076 seconds, the fastest lap ever set at the track, to beat Kimi Raikkonen and birthday boy Max Verstappen in a hard-fought session.
It was an unhappy Valtteri Bottas who finished fifth for Mercedes, ending the race 50 seconds after Verstappen.
Vettel also pitted having been unable to clear Bottas, who was left behind the German following his own stop.
The German's vehicle was badly damaged in the incident, limping along on three wheels, with Vettel then hitching a ride back to the pits on compatriot Pascal Wehrlein's Sauber.
"It's part of motor racing", said Mr. Vettel. The stewards will be looking, however, at the crash between Stroll and Vettel, to determine which driver was at fault, if any.
Ferrari and Mercedes have stepped up their interest in Max Verstappen following his Malaysian Grand Prix victory, according to the London Evening Standard.