Lewis Hamilton claimed the 40th pole position of his Formula One career at the end of a storm-hit qualifying session for the Malaysian Grand Prix that added spice to the occasion.

Thunder and lightning made for a dramatic backdrop during the initial timed run at the Sepang International Circuit before a torrential downpour unfolded midway through the second session.

After a 35-minute delay it was reigning champion Hamilton who again held sway over his rivals, but only just as the 30-year-old finished a mere 0.074secs clear of Ferrari's Sebastian Vettel, with Mercedes team-mate Nico Rosberg back in third.

There were some fun and games between Hamilton and Rosberg at one point in Q3 as the latter appeared to slow and impede the former just as the Briton had posted the quickest first sector time.

Hamilton, though, gained a small measure of revenge by passing Rosberg and then slowing himself, suggesting there are still mind games going on between the duo.

Come the conclusion Hamilton was left breathing a sigh of relief as Vettel – and not Rosberg – emerged as his closest challenger.

Hamilton said: “The first lap was quite good. It’s always difficult when you’ve not driven in the wet, with the first lap the unknown, you don’t want to take too many risks.

“So you have to get the banker lap you need and then the next one I was up at one stage, but I lost a little bit somewhere.

“In the end the team has done a fantastic job to get me up here again.”

It is the first time in 10 races Mercedes have failed to lock out the front row, offering Vettel hope of challenging the duo in the race.

“You never know. Just look outside, when it starts to rain it can mix up things,” said Vettel, the first Ferrari driver to qualify on the front row for two years.

“The car felt good in dry and damp conditions, and on long runs we looked good in practice, so we’ll see what we can do. It looks like we are a bit closer.”

Rosberg conceded he simply “didn’t drive well enough”.

He added: “I’m annoyed by that, third place is not good enough.

“For tomorrow, I’m on the clean side of the grid so that should help me pass Seb at the start.”

Red Bull duo Daniel Ricciardo and Daniil Kvyat line up fourth and fifth, with 17-year-old Max Verstappen sixth for Toro Rosso.

The Dutch youngster becomes the first teenager in 54 years to start in the top six.

Williams' duo Felipe Massa and Valtteri Bottas start seventh and ninth either side of Lotus' Romain Grosjean, with Marcus Ericsson 10th for Sauber.

Q1 unfolded just as the storm threatened, with the circuit lit up by a series of lightning strikes, whilst loud claps of thunder resounded overhead.

For McLaren, it never rains but it pours at present, as hopes of Fernando Alonso and Jenson Button making it into the second session ultimately came to nothing.

Button at least gained the upper hand over his more illustrious team-mate, pipping the Spaniard by 0.110secs.

Alonso, back in the cockpit this weekend after missing the Australian Grand Prix as he recovered from concussion sustained in an accident in testing, had suggested in practice he had the space to squeeze into Q2.

But the double world champion made a key error on his final hot lap in Q1 and will now line up 18th, with Button one place ahead of him and Sauber's Felipe Nasr 16th.

The only rainbow on the horizon for McLaren is they have improved on their opening qualifying performance in Australia, cutting the gap to the lead car in Q1 from 2.836secs to 2.262secs.

However, Button was still an eternity away in F1 terms from making Q2, finishing six tenths of a second adrift of moving into the top 15.

Despite that, Button said: “It was easier than the last race. We’ve had no issues this weekend which is good, and we’ve taken a massive step in performance.

“We’ve not challenged the other cars, but we are a lot closer. It is an improvement so we should be happy with the step.”

Alonso, meanwhile, has no doubt his Q1 exits will be short-lived as he said: “It (qualifying) was not too difficult or unexpected.

“We are struggling with the pace, but the progress with the car has been fantastic after Australia.

“I don’t think I will be talking to you after Q1 for long.”

Manor duo Roberto Merhi and Will Stevens will have to wait for the decision of the stewards to determine whether they will take part in the race.

Merhi set a time 0.460secs outside the 107 per cent mark, whilst Stevens failed to take to the track at all due to a fuel pressure problem.

Stevens would like to think he will be allowed to race as he said: “It’s incredibly disappointing for me and the team.

“I’m not sure what happens now, but personally from my side of the garage we showed we could comfortably get inside 107 per cent. The time I set in FP2 would have seen us through in quali.”

With the rain imminent the remaining 15 cars formed a queue to get out on track for the start of Q2 in order to set a timed lap.

As always with F1, just add water for excitement, and so it proved as a scramble emerged, with Hamilton only just scraping through, whilst the big loser was Ferrari's Kimi Raikkonen.

The Finn had proven Mercedes’ closest challenger in practice and seemed poised for a top-three grid slot, but will now start 11th.

Pastor Maldonado lines up 12th ahead of Force India pair Nico Hulkenberg and Sergio Perez, with Toro Rosso's Carlos Sainz Jr 15th.