Lorenzo was 0.658 seconds faster than Marquez in a single 75-minute qualifying session which was cut short because of rain at the Twin Ring Motegi track north of Tokyo.
Following Friday’s cancellation of practice sessions due to rain, riders were given a special 75-minute qualifying heat on Saturday afternoon.
“We were lucky to have the extended qualifying time to get used to the track,” Lorenzo said. “Little by little I got confidence and finally I felt really good with the bike and the grip of the track.”
The race is the 17th round of the 18-event MotoGP season. Marquez has an 18-point lead over Lorenzo and can wrap up the title on Sunday if he wins and Lorenzo finishes third or lower.
Nicky Hayden of the United States was third fastest and will join Lorenzo and Marquez on the front row.
Dani Pedrosa, Valentino Rossi and Andrea Dovizioso make up the second row.Dani Pedrosa, Japanese GP, Jorge Lorenzo, Marc Marquez, MotoGP, Nicky Hayden