NASCAR team co-owner Gene Haas set up his eponymous F1 operation in 2016, which finished its debut season eighth in the teams' standings.
Bottas was only fifth, nearly seven tenths adrift of Hamilton.
Hamilton's win moved him 28 points clear and left the Brit in a commanding position heading into Sunday's race.
Concurring Team boss Toto Wolff added: "A blistering lap, he put it all together, but we are left with some confusion because our vehicle wasn't good. So I think it's more the driver here than the auto, to be honest". "We guarantee that we will be fighting right to the final corner of the very last grand prix of the year", Ferrari team chief Maurizio Arrivabene said.
"Today we arrived and the vehicle was much better, but still I think it looked like the Ferraris were a little bit ahead. You have to look at what's coming and the vehicle is strong".
Hamilton did manage to avoid beaching the vehicle and was able to limp back to the pits, where his mechanics removed the nose and started making frantic changes to the set-up.
Red Bull Racing in particular looked comfortable in the wet morning session, with a 1.6-second margin to the next-quickest auto underlining its supremacy in mixed conditions, while Alonso's performances in both sessions - third in FP1 and fifth in FP2 - suggest the low-grip conditions could favour his McLaren.
"It is a close battle in the championship and you are looking to gain every advantage you can wherever possible. With a quick auto, you can come back, and overtaking is possible here".
"Of course it's a turning point when you go from being behind all season long and now two races being in the lead. So if nothing goes wrong with the auto then he's in a really strong position". "But I still contemplate what decisions I'll take", said Hamilton, who recently spoke of wanting to start a family.
Other news is that Daniil Kvyat has lost his seat at Toro Rosso and GP2 champion Pierre Gasly is taking his place.
"It feels wonderful, honestly".
"There is no real target". "It is sad to think this is our last race at Sepang". Race coverage starts at 6.30am on Sunday - with lights out at 8am.
Singapore offered some respite, since it was a night race, but this one is raced in afternoon heat with 80 per cent humidity.
Malaysia has hosted some epic tussles down the years.
But Daniel's first stop won't be the race track.
There has also been controversy. He can ill afford another blip in Malaysia, where the intense heat and stifling humidity make it one of Formula One's toughest races. The Australian was furious.
Who will come out on top in Sepang?
Vettel clocked 1min 31.261sec around the 5.543-kilometre circuit on his qualifying simulation run in the second session to smash the old record of 1:32.50 set by Fernando Alonso in 2005.
Sepang: Next month's Mexican Grand Prix can give the country a "moment of happiness" as it struggles to recover from its deadliest natural disaster in three decades, Formula One driver Sergio Perez said on Thursday. "I don't know whether he feels pressure".
"Fridays are when you play around and try some things", he said.
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