(updates with Raikkonen penalty)
* Vettel takes second pole of the season
* Massa on front row, ahead of Alonso
* Raikkonen loses three places on grid
By John O'Brien
SEPANG, Malaysia, March 23 (Reuters) - Red Bull's Formula One world champion Sebastian Vettel made the most of a well-timed change of tyres in a rainy qualifying session to seize pole position for the Malaysian Grand Prix on Saturday.
Vettel will be joined on the front row for the second round of the season by Ferrari's Felipe Massa, with the Brazilian outqualifying his Spanish team mate Fernando Alonso for the fourth race in succession.
Alonso, last year's winner in Malaysia and second in the Australian season-opener last weekend, will start in third place.
Lewis Hamilton will complete the second row in his Mercedes with Red Bull's Mark Webber disappointed to be fifth after getting his timing wrong in the final session.
"If you start in the front, you always want to finish there as well," Vettel told reporters after his 38th career pole and second of the season.
"It will be a long race and it's difficult to know the true pace. We confirmed what we saw in Melbourne. I'm happy with the balance of the car."
Vettel's raw pace in Australia was negated by excessive tyre wear in the race and after finishing third there, the German adopted a cautious approach in the first two rounds of qualifying on Saturday.
"It was one of those qualifyings you just want to survive," said team principal Christian Horner after the rain had caught some others out. "Q1 (the first phase) was a bit close for comfort."
The first drops fell in the second phase but the Red Bull's speed shone through once the 10 cars in the final round were all fitted with intermediate tyres as a downpour soaked half of the Sepang Circuit.
Vettel opted to change his intermediates early in the final phase and, after lapping more than a second ahead of early pace-setter Hamilton, his time was far too competitive for the two Ferraris to better as the chequered flag was waved.
"We knew that rain was on the way and we expected some at the beginning of qualifying but it didn't come so we went out on drys (tyres) and had a different approach to other people," the German added.
"We were a little on the edge in Q2 so the rain helped us a little bit, otherwise I think we may have had to go out again, but we were just fast enough to get into the final round.
"In Q3, with the circuit drying it was clear it was better to change tyres and we did that pretty early and it was the right thing."
Melbourne winner Kimi Raikkonen qualified down in seventh place for Lotus but was later handed a three-spot penalty by stewards for impeding the Mercedes of Nico Rosberg (sixth).
Jenson Button will move up to seventh, Force India's Adria Sutil to eighth and Button's McLaren team mate Sergio Perez starts in ninth.
Massa was unsure if his car was quick enough to finish as high as it did had the weather stayed dry, but the Brazilian, like Vettel, used an early change of tyres in the third phase to secure a first front row start since Bahrain in 2010.
"There were some other fast cars - Webber and also Kimi. It was a good qualifying from us, we took the right decision to change tyres so maybe the rain helped a bit," the Brazilian said.
Alonso, who finished second in Melbourne and won a rain-hit Sepang race a year ago, remains cautiously optimistic of at least scoring points from a good place on the grid.
"We are not sure about the performance of the car in terms of race pace. Every run we do is inconsistent so we need to see how the race goes," the double world champion said.
"We have not had big problems during the long runs on Friday. In Melbourne, the race pace was okay so there is no reason not to be optimistic tomorrow." (Editing by Patrick Johnston/Alan Baldwin)