The Italian took his fifth pole in the premier class of grand prix racing in a time of two minutes, 11.485 seconds to push the Yamaha riders Rossi (2:11.731) and Lorenzo (2:11.787) into second and third place on the front row of the grid.
World champion Marc Marquez, who skipped Friday's second practice after suffering from a bout of gastroenteritis, will line up fourth for the penultimate round of the championship.
The Spanish Honda rider, who secured his third MotoGP world title two weeks ago in Japan but crashed out of the Australian Grand Prix last Sunday, will be joined on the second row by Cal Crutchlow and Ducati's Andrea Iannone.
Briton Crutchlow, winner at Phillip Island last week, secured fifth place despite sliding off his LCR Honda earlier in qualifying.
Six-times MotoGP world champion Rossi leads Lorenzo, last year's champion, by 24 points in the race for second place in the standings behind Marquez.
Earlier, officials announced that Sepang would host a round of the MotoGP world championship for at least another five years until 2021.
"We have been here since 1999 and it has been a long road together," said Carmelo Ezpeleta, chief executive of rights holders Dorna.
"We're extremely proud of the Malaysian GP, the increasing spectator numbers and the incredible spectacle. We are proud to renew for at least these five years."
Malaysia is considering halting the annual Formula One Grand Prix after its contract ends in 2018 due to declining ticket sales and TV viewership.
(Writing by Nick Mulvenney, editing by John O'Brien)
