Hamilton, who won in Malaysia in 2014, said he was disappointed the race was coming to an end.
'We have to maximise every opportunity we can get, we have put ourselves in the best position possible but we will keep our heads down and behind me it will just unfold the way it is going to unfold'. "But today we arrived and the auto was much better". However, having set the pace in the wet earlier in the day, Red Bull was denied the chance to make a late push for afternoon honours when Grosjean's Haas hit the barriers at turn 13, the Frenchman having unluckily received a puncture as he ran over a loose drain.
"The auto seems to be unbalanced and that triggers an terrible lot of consequences and it was certainly one of the worst Fridays I can remember".
Vettel is a four-time victor of this race, last claiming the victory in 2015.
"We had such a hard day yesterday, it was hard to know where we stood", Hamilton said.
After going out on the first lap at the last round in Singapore, Vettel suffered a huge setback to his championship hopes. The team split its set-up for final practice, and continued that approach for qualifying, with Valtteri Bottas running an updated aero package and Hamilton reverting back to the older spec W08. "It's a shame that we couldn't get out". We have more tyres than everybody else, we can maybe do something with strategy and then for sure if the Safety Car comes out at a time that suits you, you might come back and you never know what's possible.
But the Malaysian government said in April that this year's race - which takes place on Sunday - would be the last. "So we need some answers", Wolff said.
That leaves the Mercedes team with plenty to do to beat Ferrari and Red Bull to pole position in Malyasian GP qualifying on Saturday.
With Vettel at the back of the field, Raikkonen will lead Ferrari's charge after missing out on pole by a mere 0.045 seconds.
"I had a couple of hard race weeks for myself in the last few weeks but really hoping to lift my performance this weekend", said the 28-year-old driver from Finland.
'It is always a special thing when you are able to extract a little more out of the auto than it is willing to do'.
The second Mercedes of Valtteri Bottas was fifth, with Esteban Ocon completing the top six in his Force India.