Pre-season pacesetter Ferrari had a subdued session, lapping well off the pace early in the session on medium-compound Pirellis, with Sebastian Vettel complaining over the radio that something felt wrong in Turns 1 and 4.
Vettel may need to produce something special to claim a third straight Australian GP after struggling at second practice.
The man Leclerc replaced, Finnish former world champion Kimi Raikkonen, pushed his Alfa Romeo - formerly Sauber - into sixth.
Mercedes and Lewis Hamilton claimed the Formula One titles in 2018 yet appeared pessimistic ahead of the new campaign, with Vettel's Ferrari impressing in testing in Barcelona.
Hulkenberg's time signified a much more competitive showing for Renault than in FP1, with Daniel Ricciardo less than 0.1s further back on a 1m23.644s.
Catherine gives rare update on Prince Louis on special day out
Supermodel Kate Moss was pictured heading home with her beloved boyfriend Count Nikolai von Bismarck on Tuesday night. Back in June previous year we first heard that he was crawling when the Duke and Duchess visited Dundee in Scotland.
"By the time you finish the testing, the cars are ready to be shipped directly to Melbourne, so I think it's really by here that we start understanding who is the fastest".
"When we get to Q2 and they start to crank the engines up, that's when the story will start to unfold of where are Honda".
Bottas said the auto felt better than during testing. The forecast is for warmer conditions for Saturday's qualifying and Sunday's race. "So, in the end we're racing for Ferrari and that means we try to get Ferrari back to where we've been trying to get it back to for the last couple of years". It's how Formula One cars are supposed to be when they're wide and they're big.
The German said afterwards it had been "a tricky day". I think for us we are not where we would like to be, not in terms of lap time but in terms of vehicle feel and handling. "We didn't really get into the groove and the rhythm".
The German won the opening race of the season in Melbourne previous year and backed it up with victory at the next in Bahrain.
The other rookie, British-born Thai Alexander Albon, had a hard first day.
FIA chief Jean Todt held a minute's silence to mark his passing in a press conference, with deputy race director Michael Masi fulfilling Whiting's duties in Melbourne.