The Mercedes driver notched up the best lap of the day after changing from the slower medium compound to soft tires.
Yet his time of one minute, 23.022 seconds was still marginally slower than that achieved by team-mate and 2014 driver's championship rival, Nico Rosberg on the soft tires on Friday.
The Englishman later told reporters he would have liked more laps having missed last week's practice session due to illness but was content with how the car was performing.
"It's been generally good," Hamilton said in quotes carried by the AFP news agency. "The team has done a great job to get all the components here and reliability has been strong. We are in as good a shape as we can be."
Mercedes were by far and away the dominant force in F1 last year and there was little indication Saturday that this will not be the case in 2015.
Williams were the closest challengers, as they had been on Friday, with Felipe Massa finding his best time of the testing season.
But this was still fully two tenths of a second down on Hamilton despite Massa being on the faster super-soft tires at the time.
Ferrari's Kimi Raikkonen clocked third fastest time of the day, marginally over one hundredth of a second behind Massa.
McLaren-Honda troubles continue
Saturday proved yet another unhappy day for the CNN sponsored McLaren-Honda team as reserve driver Kevin Magnussen's participation was cut short after his car suffered an oil leak.
Magnussen was standing in for Fernando Alonso who suffered concussion after crashing last Sunday.
"The day stopped a little too early for us," said McLaren racing director Eric Boullier.
"We didn't do as many laps as we wanted. It is true it is going to hurt the development of the car on the performance side, but we will recover."
The F1 season gets underway in Melbourne on Mar