To make matters worse, Sebastian Vettel, who lies 28 points behind Hamilton in the race for the drivers' title, smashed the all-time Sepang lap record in his Ferrari, lapping more than 1.4 seconds quicker than the Mercedes.
Hamilton, who suffered a similar championship setback to Vettel a year ago in Malaysia when his engine blew while he was leading, was also reluctant to hail the Singapore race as the season's decisive turning point.
Bottas said after qualifying he regretted sticking with Mercedes' new-for-Malaysia aero updates following the team's disastrous Friday showing, while Hamilton reverted to the older specification overnight.
Ferrari entered Saturday's qualifying running as the favorite for pole following a strong showing in practice, only for an engine issue to sideline Sebastian Vettel from the session entirely.
Formula One championship leader Lewis Hamilton was handed a lucky break in Singapore but the Mercedes driver can take little more than the heat and humidity for granted in Malaysia this weekend. "Quite the contrary. I have been working very hard in the past few years to make it to F1 - why should I crack now?"
Concurring Team boss Toto Wolff added: "A blistering lap, he put it all together, but we are left with some confusion because our auto wasn't good".
"The race is tomorrow not today. The lap time today showed that we are not quick enough", he told reporters.
"Obviously the race (at Singapore) didn't go that way but I don't see why you would look at everything so negative".
Hamilton won four of the five races after Malaysia past year but it was still not enough to stop team mate Nico Rosberg taking the title.
"For the record I still think we should host MotoGP.1) Cheaper fee and cost, 2) Sell-out crowd, 3) We have riders in Moto2 and 3". "It is one of the worst Fridays I can remember".
"But we've not been very good at high speed here".
"As a team we want to get maximum points with two cars".
"When you get that close it's a disappointment", said Raikkonen.
Eddie Irvine won the first-ever Malaysian Grand Prix in 1999 - the Northern Irishman's fourth and final F1 victory - while in 2003, Fernando Alonso finished third to claim the first of his 97 podiums.
"The easiest part is to come back and negotiate with Liberty Media for F1 to come back", he concluded.