This was Yamaha's first win at the prestigious event since 1996.
The Tech 3 MotoGP team-mates Espargaro, Smith and factory test rider Nakasuga won by 1m 17.411s ahead of the rest of the field. This included a penalty of a 30-second stop and go in the middle of the race.
In second place were Dominique Aegerter, Josh Hook and Kyle Smith of TSR Honda.
Team Kagayama, made up of Yukio Kagayama, Ryuichi Kiyonari and Noriyuki Haga came in third, one lap behind the winners.
Defending champions The Musashi Honda team were forced to pull out of the event when Casey Stoner crashed damaging the bike and breaking his arm and fracturing his leg.
For Bridgestone this was their 10th consecutive win of the legendary race.
Results – Suzuka 8 Hours:
1. Nakasuga/Espargaro/Smith – Yamaha Factory Racing #21 204 laps
2. Aegerter/Hook/Smith – FCC TSR Honda #778 1m 17.411s
3. Kagayama/Haga/Kiyonari – Team Kagayama Suzuki #17 -1 lap
4. Philippe/Delhalle/Masson – Suzuki Endurance Racing Team #30 -2 laps
5. Tsuda/Lowes/Waters – Yoshimura Suzuki #12 -3 laps
6. Checa/Foray/Gines – GMT94 Yamaha #94 -3 laps
7. Costa/Gimbert/Foray – Honda Endurance Racing #111 -3 laps
8. Hiura/Kamei/Yasuda – Honda Suzuka Racing Team #25 -4 laps
9. Yanagawa/Yudhistira/Watanabe – Team Green Kawasaki #87 -5 laps
10. Konno/Aoki/Ogata – Motomap Supply Suzuki #32 -5 lap