The Briton's fastest time was just over three-tenths down on Leclerc's who secured the first pole position of his Formula 1 career.
Two weeks ago, Mercedes dominated proceedings in Melbourne, taking a front-row lockout and securing the one-two finish in the race, with Hamilton following his teammate Valtteri Bottas home by over 20 seconds.
But after a difficult Friday in Bahrain, Hamilton believes Mercedes has recovered well and will be in a strong position in the race to challenge Ferrari,
“Yesterday was a struggle,” said Hamilton after qualifying. “All weekend, we’ve seen incredible pace form Ferrari, and I didn’t know we would be as close as we were.
“I made changes to the car overnight, so I’m hopeful the car is in a better position. It’s why I‘m a bit more upbeat,” he added.
“Now we are in a better position. Tomorrow’s the more important day and it will be interesting to see how we do. We’re going to give them a good fight, that’s for sure.
"They’ve showed incredible pace but it doesn’t mean they can’t be beat. We’re going work on it, keep our heads down and see what happens.”