Briton Hamilton claimed a record-extending eighth pole position at Albert Park on Saturday but ended up a distant second to his resurgent team mate Valtteri Bottas, who got the jump on him at the start and burned away.
Hamilton was called in to pit early and change to medium compound tyres, straight after Ferrari's Sebastian Vettel did the same.
Bottas, meanwhile, stayed out on his soft tyres and extended his lead.
With Red Bull's third-placed Max Verstappen a menacing presence behind him, Hamilton complained on the team radio that he was worried his tyres would not last and battled handling issues late on.
He later found out there was a piece of his floor missing which would have exacerbated his car's balance problems and so did well to hold on to second to the finish.
Maximum points for Mercedes was a great team result, but Hamilton was condemned to finishing runnerup for a third year in a row in Melbourne, after losing to Vettel in the last two editions.
Overall, Hamilton has converted only two of his eight poles into wins at Albert Park, in 2008 and 2015, a record which would frustrate the most tranquil of drivers.
"Obviously the strategy was not ideal in the scenario that I had," he told reporters of the early tyre change.
"So working with what I was given, I think I did a relatively decent job.
"Just obviously the start, I lost out quite a lot."
Mercedes boss Toto Wolff said it was the right decision to have Hamilton pit early.
"No, I don’t think it was a mistake because we could have ended up behind Vettel, not doing that," he said.
"I don’t know why they pitted (Vettel) so early. That put us under pressure, we needed to cover that undercut."
While Hamilton's day was tinged with disappointment, Mercedes were thrilled their raw pace was more than enough to put Ferrari and their rivals out of the equation.
Both Vettel and his new team mate Charles Leclerc finished nearly a minute behind Bottas, a performance that surprised the Silver Arrows.
"I think we were surprised that we had such a good pace and we were surprised that they didn’t have any pace at all," Wolff said.
"And maybe the truth is somewhere in the middle."
(Editing by Amlan Chakraborty)
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