Having lapped 0.293s off teammate Lewis Hamilton, who took pole for the Australian GP, Bottas was then denied a front row start by Ferrari's Sebastian Vettel in the dying seconds of the final segment.
Evidence in testing was that the heavier, more aerodynamic cars could corner faster and were significantly faster than the 2016 edition.
The three-time champion vented increasing frustration at Mercedes during key moments of his tense title battle with Nico Rosberg, making repeated reference to the lion's share of reliability woes he suffered over the course of the season in comparison.
Kimi Raikkonen will lead the supporting cast as he starts from fourth for Ferrari, with Red Bull's Max Verstappen fifth.
Mercedes teammate Hamilton had attempted to back Rosberg into the chasing pack as he looked to snatch the championship away. "The vehicle doesn't yet feel as good as it should and as it can", said the German.
The race lasts 58 laps, covering a total distance of 191.118 miles.
"It has put us in great stead for tomorrow", he said.
Unlike Ferrari, Mercedes chose to wait until later in the session to complete its runs on the ultra-soft tyre.
The Australian carried a little bit too much speed into the corner and as he approached the apex the rear started to overtake the front, slewing the auto out towards the gravel. The driver who replaced the world champion, Valtteri Bottas, lines up in third.
Daniel Ricciardo qualified 10th after spinning off at Turn 14 on his fast lap and rear-ending the barriers.
Hamilton posted the fastest times in the first two practice sessions but was nearly a half-second behind Vettel in the third practice on the 5.303-kilometre (3.295-mile) circuit, giving Ferrari some genuine hope of returning to pole position.
"Third is not ideal - I think in general I'm not happy for the result", said Bottas, whose previous best qualifying in Australia was sixth.
Red Bull's Max Verstappen qualified fifth but it was a forgettable day for his team mate Daniel Ricciardo, whose hopes of becoming the race's first home victor spun out early in Q3.
Sixth on the grid went to Romain Grosjean in the Haas F1, while Felipe Massa took seventh spot on the grid for Williams. Missing out on that wasn't a major setback, considering Ferrari is confident of being fast off the grid. "Hopefully we can kick off well".
That wound up being the last of the significant improvements in the top order, as a Lance Stroll crash sparked the first red flag of the day when he hit the wall at the exit of Turn 10.
Antonio Giovinazzi will start 16th on his debut for Sauber after an impressive showing with just one practice session of experience behind him. The Briton stamped his authority in the first qualifying session of the season, by setting a record breaking lap of 1 minute and 22.188 seconds.