The Spaniard's Yamaha team mate Valentino Rossi qualified alongside, marking his return to his home circuit in eastern Italy with a special 'Sweet Home Misano' Blues Brothers-themed helmet design.
Spaniard Maverick Vinales, who is replacing Lorenzo at Yamaha next season when the champion switches to Ducati, qualified third for Suzuki after winning the previous race in Britain.
The pole was the fastest yet at the Marco Simoncelli circuit in eastern Italy and Lorenzo's 64th in grand prix racing, a record he had previously shared with Rossi and Honda's championship leader Marc Marquez.
"You always have the impression that the last pole position is the best of your life but I really think that this one is," said Lorenzo after lapping in one minute 31.868 seconds.
Marquez qualified fourth fastest.
(Reporting by Alan Baldwin, editing by Ed Osmond)
