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The FIA World Endurance Championship leading #8 Toyota TS040 Hybrid of Anthony Davidson and Sebastien Buemi will start on pole position for the Fuji 6 Hours after snatching the initiative away from Porsche in qualifying.
Porsche appeared on course for its second pole position of the season when Timo Bernhard and Mark Webber's respective laps gave the #20 919 Hybrid a comfortable average advantage over the competition.
However, a last gasp effort from Buemi would see the #8 Toyota squeeze ahead at the last moment by less than a tenth around Toyota's home venue, the Swiss driver doing the honours alongside sole team-mate this weekend Davidson, the pair sharing the car as a twosome in the absence of Nicolas Lapierre.
A strong session for the Porsche team, which is still seeking its first WEC win of the season, the #14 car of Neel Jani, Romain Dumas and Marc Lieb followed in third, with the #7 Toyota of Alex Wurz, Stephane Sarrazin and Kazuki Nakajima completing the second row.
Audi, having dominated free practice, continued its format of focusing on race pace, with the #2 R18 leading the sister #1 car in fifth and sixth positions.
In the LMP1-L class, the Rebellion of Nicolas Prost, Nick Heidfeld and Mathias Beche lead the way in seventh overall, ahead of the sister Rebellion car, while sole rivals Lotus could only manage 14th overall.
G-Drive headed up qualifying in the LMP2 class from the wildcard OAK Morgan Judd, which includes local driver Keiko Ihara, with KCMG and the SMP Racing machines following in third, fourth and fifth.
In the GTE classes, Aston Martin were the dominant manufacturer, with Alex MacDowell, Fernando Rees and Darryl O'Young securing its first GTE Pro pole position from Darren Turner and Stefan Mucke in the sister V8 Vantage, while the leading AF Corse Ferrari of Gimmi Bruni and Toni Vilander could only manage fifth. Similarly, GTE Am saw Pedro Lamy, Paul Dalla Lana and Christoffer Nygaard lead the way in their Aston Martin.