Although Ferrari took a convincing 1-2 in qualifying at the Italian GP two weeks ago - Raikkonen ahead of Vettel - Vettel spun off track after a shaky start and finished fourth to concede more ground.
While Vettel was critical of Ferrari's strategy calls in Singapore on both Saturday and Sunday, Hamilton was full of praise for his Mercedes team after their unexpected triumph at what was considered to be a bogey track for the world champions.
Hamilton got the flawless start from pole position as Verstappen was slower away from second on the dirty side of the grid and saw his Red Bull come immediately under pressure from Vettel.
"No we are looking good compared to those around us", assured his race engineer Peter Bonnington.
Asked if he had concerns that the engine might fail in the race, Verstappen added: "No, I think in the race you have to turn down the power anyway - it's just when you go to the limit of the engine, we seem to struggle somehow with drivability and torque mapping".
"Then I must really take my hat off to the work that was being done in the United Kingdom, in Brackley and in Brixworth to prepare the vehicle and the engine for this race because, together with Monaco, it is our weakest race track".
Lewis Hamilton extended his championship lead to 40 points. Rather than gaining an advantage, Vettel was released into traffic and ended up falling behind Max Verstappen's Red Bull.
For the remainder of the race, Vettel found ended up unable to improve on third place. I needed to shift very quickly in order to get back into a gear.
"I'm spent", Hamilton said moments after victory, crouching down by his auto.
"It's so hard to overtake here", Hamilton said. His middle sector had been 0.110s quicker than Hamilton's, giving Verstappen a shot at pole had he had a clean final sector of the lap, but he was forced to abort his lap after the issue. We almost dropped out in Q1 after sticking to the UltraSoft tyre, which was a nerve-wracking wait to make sure we didn't shoot ourselves in the foot at the first opportunity.
Verstappen was the next in, nearly colliding again with Vettel into turn 3. Mercedes pitted Hamilton moments later, and when Vettel came back out he was still behind Hamilton and lost more time getting past Perez.
Hamilton aced the restart to resume the race, but the first stint proved tepid at best while the top 10 cars tried to extend the life of their delicate hypersoft tires as far as possible. Verstappen held position, Vettel dropping to third.
"It was clear we were not fast enough in the race, we need to understand why".
"We knew that they would be spectacular here this weekend and so it was going to take something quite special for us to leapfrog them", he said.
Time is running out for Vettel, who realistically has to win in Russian Federation in two weeks' time if he is to get back into title contention.