Lewis Hamilton on pole for Malaysia GP from Sebastian Vettel

Lewis Hamilton has taken pole position for the Malaysia GP ahead of Sebastian Vettel and Nico Rosberg.

The world champion set a time of 1:49.834 on the 5.543km track, which was drying after a thunderstorm midway through the session caused a delay.

He will therefore start on Sunday ahead of Vettel, who ended Mercedes' string of nine front-row lock-outs with a time just 0.074s slower, although Hamilton set his time on his first flying lap.

Rosberg lines up third - the first time he hasn't been on the front row since Austria last year - although the German had clearly hoped to get the best out of the conditions by positioning his car to be last across the line in the closing seconds.

Hamilton was on a timed lap moments before, but had to back out of it when he came up behind the other Silver Arrow.

Now ahead of Rosberg, he still had time to make another attempt. Hamilton didn't improve, but his earlier lap - set several minutes earlier on a drying track - was sufficient. 

"The first lap was quite good," Hamilton said afterwards. "It's always difficult because none of us had driven a lap this weekend in the wet. The first lap is just the unknown and you don't want to take too much risk that you don't get the lap. But you need a banker. My lap was feeling pretty good, so I was pushing.

"The next one was up at one stage and then just lost a little bit on the lap, but generally a fantastic job from the team to have us up here [in the top three] again."

“It was an interesting qualifying session," said Vettel. "The car felt good in dry and wet conditions and also the long runs looked good in practice.

“But we know they [Mercedes] are difficult to beat, but ultimately that is why everyone turns up to try to win. We will see what we can do tomorrow, it looks like we are a little closer here, but we will wait and see.”

Rosberg said: "I just didn't drive well enough and I'm annoyed by that. Third place isn't good for tomorrow but it is what it is.

"For tomorrow I'm on the clean side of the grid so maybe that should definitely help me to get by Sebastian at the start."

Red Bull pair Daniel Ricciardo and Daniil Kvyat start fourth and fifth ahead of Toro Rosso's 17-year-old Max Verstappen, who becomes the youngest driver since 1961 to qualify so high up the grid.

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Felipe Massa was seventh for Williams ahead of Lotus's Romain Grosjean, although the Frenchman drops two places behind Valtteri Bottas (Williams) and Marcus Ericsson (Sauber) to 10th on the grid after a pitlane infraction.

Losing out, therefore, was Kimi Raikkonen, who had matched team-mate Vettel all week so far but lost out when the rain hit.

Storm clouds had been gathering as the session got underway and with spectacular lightning bolts in the air during Q1, the rain arrived shortly after Q2 started.

There was just enough time for cars to complete a run on dry tyres, but in the rush to set a time both Hamilton and Raikkonen found themselves amid a gaggle of cars led by Ericsson.

With Rosberg fastest at this stage, Hamilton squeezed into the top 10. “You guys got us out too far behind everyone, man,” he told his crew, who replied that they hadn't been able to fire his engine up properly. 

But Raikkonen didn't and was as downcast as the weather. “There’s not much that I can do," he told Sky Sports F1. "There’s always a chance to have a difficult first few corners if you are out of place. Also it takes our chances away.” 

Even so, the expectation has to be that Raikkonen will make rapid headway in the race. He lines up 11th ahead of Pastor Maldonado (Lotus), Force India pair Nico Hulkenberg and Sergio Perez with Carlos Sainz (Toro Rosso) and Felipe Nasr (Sauber) next up.

At least McLaren, who qualified on the back row in Australia, will line up ahead of Manor this time with Jenson Button 17th ahead of Fernando Alonso.

But they insist they’re happy with progress. “It was expected. Obviously it’s a tough period at the moment for us, being out of Q1, but the number are much better than Australia in terms of pace, so I think we are making very big progress,” a smiling Alonso told Sky Sports F1

The Spaniard joked: “If we can improve 1.5s every two weeks then in three or four races we’ll be on pole. So we’ll see.”

Both Manor cars have been allowed to race at the discretion of stewards under the 107 per cent rule. Although Will Stevens didn't take part because of an electrical problem with his car's power unit, he was fast enough during practice.

Roberto Merhi did take part in Q1 and will start despite being 7.4s slower than pacesetter Hamilton.

Result:
1) Lewis Hamilton, Mercedes, 1:49.834
2) Sebastian Vettel, Ferrari, 1:49.908
3) Nico Rosberg, Mercedes, 1:50.299
4) Daniel Ricciardo, Red Bull, 1:51.541
5) Daniil Kvyat, Red Bull, 1:51.951
6) Max Verstappen, Toro Rosso, 1:51.981
7) Felipe Massa, Williams, 1:52.473
8) Valtteri Bottas, Williams, 1:53.179
9) Marcus Ericsson, Sauber, 1:53.261
10) Romain Grosjean, Lotus, 1:52.981 *
11) Kimi Raikkonen, Ferrari, 1:42.173
12) Pastor Maldonado, Lotus, 1:42.198
13) Nico Hulkenberg, Force India, 1:43.023
14) Sergio Perez, Force India, 1:43.469
15) Carlos Sainz, Toro Rosso, 1:43.701
16) Felipe Nasr, Sauber, 1:41.308
17) Jenson Button, McLaren, 1:41.636
18) Fernando Alonso, McLaren, 1:41.746
19) Roberto Merhi, Manor-Marussia, 1:46.677
* received two-place grid penalty