The opening segment of qualifying was completed after a delay but, as the rain persisted and the skies grew darker, race officials decided the final two parts would take place on Sunday morning.
After a bright, sunny morning at Albert Park, the rain descended in time to disrupt the final practice session and rarely relented after that.
Hamilton was the first driver to set a lap time but his day almost came to an end on his next lap when he spun his Mercedes at turn two and bumped into the tyre wall before appearing to get bogged down on the trackside grass.
The former world champion finally managed to get his car back on the track and, despite his team fearing he had rear wing damage, stayed out on the track to record the 10th quickest time.
"It's not been a good weekend so far, lots of down points so far but I think we can turn it around," he said.
"It was not the best of situations to be in but at least I didn't take any wheels off. I was able to keep going. It wasn't very good."
That set the trend for the session as car after car spun off with Ferrari's Felipe Massa, Jenson Button's new McLaren team mate Sergio Perez and Dutchman Giedo Van der Garde all losing chunks of their car.
Race director Charlie Whiting came to the conclusion hat there was no option but to delay the qualifying.
It was the first time since the 2010 Japanese Grand Prix that bad weather had caused qualifying to be held on the same day as the race and McLaren star Button said it was disappointing for driver and spectator alike.
"There's so much pent-up energy and adrenalin and we've got to find a way of getting rid of that now," said Button, who has won three of the last four races at Albert Park.
"It's sad for the fans, they've been here all day and we weren't able to put on a show."
The first section of qualifying started with plenty of water still on the circuit and ended with more rain and bits of car strewn across the track as the drivers struggled to control their machines.
Nico Rosberg of Mercedes set the quickest time in that session in one minute 43.380, ahead of Ferrari's Fernando Alonso and Romain Grosjean in a Lotus.
"I don't want to think too much about the front row," said Rosberg. "For sure, it's going to be much more difficult in the dry. Today we were really quick in the wet ... in the wet, great car."
Button escaped an embarrassing exit by making an early gamble on intermediate tyres but Pastor Maldonado of Williams was late to make the change and was one of the six drivers eliminated.
The Venezuelan, a race winner last year in Spain, was accompanied by four of the five rookies but was not about to blame the weather for his early exit.
"We need to work very hard to solve the problems," he said. "The car is undriveable at the moment."
Sauber's Esteban Gutierrez, the Marussias of Jules Bianchi and Max Chilton as well as Caterham driver van der Garde were also eliminated.
Charles Pic had a big crash before the end of the session and failed to record a time inside 107 percent of the quickest in his Caterham and so will have to appeal to the stewards to race on Sunday.
There was no complaint from the teams about the delay.
"I think it was absolutely the right decision to delay it until tomorrow morning," said Red Bull team principal Christian Horner. "It's a shame, but I think Charlie has made the right call.
"You can see it's quite dark now and these conditions are not safe for the drivers. Hopefully this weather will blow through tonight and we'll be back with better conditions in the morning."
That view was echoed by Alan Permane, trackside operations director at Lotus.
"I absolutely think it's the right thing to do, to delay it until tomorrow," he said.
"The two sessions will finish by 11.35 or something and that will give us plenty of time before five o'clock."