The 22-car Formula One field enjoyed just 20 minutes of dry running at the start of the hour-long session in which they managed only a handful of meaningful laps before the rain hit Melbourne with a sharp deluge.
The rain did ease off, but with more forecast around qualifying, after a pause of 15 minutes the teams sent their drivers back out for the final 25 minutes to understand the track in wet conditions.
It meant the leading times were all done in the dry, with Lotus' Romain Grosjean at the top of the timesheet, but with his lap of one minute 26.929secs a second behind Sebastian Vettel's best from Friday.
That was due to the fact no driver had an opportunity to switch to the faster of the Pirelli tyre compounds being used this weekend, the supersofts.
Reigning three-time champion Vettel, who set the fastest time at the end of both 90-minute sessions on Friday, finished 12th quickest.
Crucially, the 25-year-old German was forced to sit out the last 10 minutes with a hydraulics problem that saw him pull his Red Bull off track after being told to do so by the team.
Depending on the exact technical nature of the issue, Red Bull could face a race against time to rectify the RB9 ahead of qualifying for which he was looking favourite to grab pole position.
Come the conclusion to the session there was a dry line forming, but not enough for any of the teams to switch to a late blast on the dry tyres.
Behind Grosjean, and with times largely irrelevant, the Ferraris of Fernando Alonso and Felipe Massa were second and third on the timesheet, with Force India's Paul Di Resta up in fourth, 0.604s behind Grosjean.
In a topsy-turvy field, Lotus' Kimi Raikkonen was 0.696s adrift in fifth, with Mercedes' Nico Rosberg 1.5s down in 11th, with Vettel a place behind, but with a gap to Rosberg of 1.3s.
Mark Webber in his Red Bull was 13th, whilst McLaren duo Jenson Button and Sergio Perez were 17th and 18th, frustratingly losing valuable dry running after team principal Martin Whitmarsh yesterday admitted they were struggling.
At the bottom of the standings were Marussia's Max Chilton, with Lewis Hamilton last of all, but only he because he failed to set a time in the dry in his Mercedes.