Hamilton looked to be on his way to a fourth consecutive victory and eighth of the campaign until Red Bull’s Max Verstappen overtook the race leader in superb fashion on the fourth lap.
The Dutchman held his position ahead of Hamilton at the front of the pack to secure his first win of the year having reached the podium only once before in 2017.
With Mercedes now boasting a 118-point advantage over Ferrari, the result has done little to hurt their championship credentials.
However, Toto Wolff has identified an issue of grave concern after their fastest car finished no less than 12 seconds behind the winner.
“I’m very down,” the Mercedes chief told Sky Sports.
“You cannot look at it and say we have scored more points than Ferrari – we have lost so much pace this weekend.
“We were half a second down on Ferrari [per lap] and probably if Max had pushed to the end we would have been half a second down on Max.
“How can a car that is so fast on many circuits lose so much with the tyre that is overheating?
“In Singapore we were really good in the wet. At the moment is about keeping calm and trying to analyse it.”
Chasing a speed boost after their sluggish showing in Malaysia, Wolff and his team have just four days to devise a strategy before the Japan Grand Prix next weekend.
“If you look at the real pace today it would have been P5 and that is worrisome. We have a couple of days in Suzuka, a completely different climate, and we will know more by then.
“On paper Suzuka should suit us.
“There were some question marks over Malaysia – we should have been quicker than we were but Suzuka should be much more in the window.
“Once I have digested the race I will think about the six points we have gained over Ferrari but right now it’s still sore.”
While Mercedes can probably afford a slip-up or two at the five remaining events this year, it’s clear they want to wrap up their title defence sooner rather than later.