Hamilton, a three-time world champion, then produced a flawless performance to increase his standings lead over Vettel to 28 points with just six races remaining - starting at the Sepang International Circuit on Sunday.
"I mean, considering [Vettel] started last it's not that great, to be honest", Hamilton said, referring to Vettel's stellar drive back to fourth.
The Finn, who was set to start alongside Hamilton on the front row, was wheeled back into the pits and never returned to the track - effectively handing Verstappen second place at the start. Moments before the race, mechanics wheeled Raikkonen's auto back to the garage but could not get it ready.
It was an exciting end to Sepang's final qualifying session, as Lewis Hamilton claimed his record-equaling fifth pole in Malaysia, and the 70th of his career.
Back to the race on Sunday, the weather may well play an important part as it did previous year, when it was won by Daniel Ricciardo in his Red Bull. Nico Rosberg had been on pole position in his Merc.
One of those title-defining memories came here a year ago as Lewis Hamilton suffered an engine failure while leading the race.
Frenchman Pierre Gasly, drafted in as a replacement for under-performing Russian Daniil Kvyat at Toro Rosso, limbered up for his first Formula One qualifying session with the 16th-fastest time, one place behind team mate Carlos Sainz.
But, even with Vettel out of contention it did not come easy, with Mercedes having struggled all weekend to extract pace from their auto.
"Red Bull looked very fast in the mixed conditions this morning, in the damp and wet on the intermediate tyres", added Vettel.
Despite feeling unclear about the long run pace Force India possesses this weekend after the disrupted practice sessions on Friday, Perez feels the team are well placed to score more points in Malaysia and cement their fourth place in the Constructors' Championship.
Hamilton won four of the five races after Malaysia previous year but it was still not enough to stop team mate Nico Rosberg taking the title. "We have to make our vehicle work in every conditions but at the moment it's not working as well as some of the other cars in these conditions".
"Overtaking here is more straight-forward but, if you have a quick auto you can produce big drivers, let's see where it can take us". "I've just got to make sure I keep performing as I have been".
"It's a bit more painful when you get that close", the softly spoken Finnish driver said.
Moments later, Lewis Hamilton dipped the first kerb at the Turn 7/8 double-right and lost the rear, pitching him into a spin and across the gravel.
"I said to the guys in the garage, don't worry".