Mercedes had struggled all weekend to make their auto work at Sepang, and despite starting and leading away from pole position, Hamilton was passed by Verstappen on lap 4 and eventually finished in second place, 13 seconds behind the Dutchman.
"The auto was unbelievable, if I had to speed up I could. It is unbelievable, a very tough race but of course it is incredible to win".
Hamilton admitted the Mercedes had been second-best.
"Obviously Max got the big one and drove well so congrats to him for the win; he drove strong all weekend".
"In the beginning, the vehicle felt good and I saw Lewis was struggling a bit " Verstappen said. "It was a much better weekend than we had anticipated after our Friday".
"I think the whole race went well, once I got past Lewis I could focus on my pace and look after the tyres".More news: No. 1 Alabama vs. Ole Miss: Game outlook, where to watch, listen
Earlier in the day, FP3 was dominated by Ferrari, with Mr. Raikkonen setting the fastest time ahead of Mr. Vettel, who's engine broke down at the end of the session and could not be replaced in time for a qualifying run. But Vettel caused a crash that took out both Ferraris, and two other cars, and handed the initiative to Hamilton. I think we felt we would be in good shape. "I'm pretty certain I would have had a very good vehicle today", a disappointed Raikkonen told reporters.
Hamilton, who now leads the championship race with a 34 point advantage over second-placed Sebastian Vettel, said it was decent result considering issues he faced with his auto.
I think tomorrow is a long race, it's going to be tough for tyres and I think we should have a very good vehicle tomorrow.
"On one lap the underlying problem we had in the auto was not as obvious as it was during the race".
Once past Hamilton, Verstappen started to pull away and by lap 14 he had a seven-second cushion.
It's worth mentioning that Sebastian Vettel, who began dead last, carved his way up the field, passing rivals easily and eventually crossing the line in 4th place behind 3rd place man Daniel Ricciardo and 2nd placer Lewis Hamilton.
Bottas wished to help Hamilton but Vettel pitted on the 28th lap for a successful undercut.
Once the chequered flag had fallen he was cruising back to the pits when he somehow managed to collide with the Williams of Lance Stroll, ripping the rear wheel of his vehicle off and leaving him stranded out on the circuit.
"That's impossible", Vettel thundered over the radio. "Stroll's not looking where he's going".