The 23-year-old Spaniard put in the fastest lap at the windswept Phillip Island circuit in one minute 41.146 seconds on his Fiat Yamaha.
Lorenzo was 0.334 seconds quicker than Australian Casey Stoner (1:41.480), who is bidding for his fourth consecutive home MotoGP success riding his Ducati on Sunday.
“Today was the first day on the bike after we won the title and I am still very happy,” Lorenzo said.
“We can’t stop now, we have to keep going and finish this season in the best way possible, working for the future.”
Stoner’s American teammate Nicky Hayden was third-fastest, 0.485secs down, with 1:41.631.
Seven-time world champion Valentino Rossi was seventh best with 1:42.626, some 1.480secs slower than his Yamaha teammate Lorenzo.
“This weather was unbelievable and it was really at the limit of what you can race motorcycles in today,” Rossi said.
“I hope it will be better tomorrow. My setting here in the wet was okay and I feel quite happy on the bike, but I didn’t want to push too hard in these conditions.”
Spain’s Dani Pedrosa, second in the championship and back after missing two races with a fractured collarbone, did not post a qualifying time in his seven laps on a Repsol Honda.
Practice for all classes was delayed for two hours after overnight and morning rain left pools of water across the track and conditions were deemed too dangerous.
Qualifying takes place on Saturday ahead of Sunday’s MotoGP, the third-last race of the season.
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