The Yamaha rider cranked up the pace in the closing stages of Saturday's session to clock a record lap of two minutes 0.334 seconds and snatch his seventh pole position of the season ahead of title rival and fellow Spaniard Dani Pedrosa (2:00.528).
While it was uncannily similar to his pole-grabbing display in Japan last week, Lorenzo will be hoping to prevent a repeat of the Motegi race in which Honda's Pedrosa recorded his fourth win in five races to maintain his late-season title push.
Despite a strong start to the session, Lorenzo dropped off the provosional front row as Pedrosa grabbed the lead, surrendered it to Andrea Dovizioso and wrested it back, only to lose it again in the dying minutes.
Lorenzo reclaimed top spot from Pedrosa with a stunning 2:00.438 and followed it with a flying final effort to set a new pole record at the circuit.
"We need to still work a little on our pace as it's not extremely good yet but we have some options for tomorrow," Lorenzo said.
"Let's see what happens, it's going to be a long race in difficult conditions," predicted the 25-year-old rider.
Pedrosa had a similar complaint.
"It was hard because we had a lot of chattering this afternoon and it was very difficult to get a clean lap as in some areas the bike was chattering too much, even in the straight," said the 27-year-old rider.
"Nevertheless, we managed to get on the front row again and the second position is good," he added.
Lorenzo's team mate Dovizioso (2:00.567) finished third on the timesheets as Yamaha squeezed two bikes on to the front row.
Australian world champion Casey Stoner (2:00.811), still lacking speed following an ankle injury, struggled with the set-up of his Honda but still led the second row, ahead of the Yamaha duo of Briton Cal Crutchlow and American Ben Spies.
Lorenzo leads the championship standings on 310 points to Pedrosa's 282 with Stoner a distant third on 197.
The Spaniard sealed his sole world title at Sepang in 2010 and can repeat the feat should he win and Pedrosa fail to finish, with just two rounds remaining after the Malaysia race.
- Dani Pedrosa