Jorge Lorenzo produced a blistering late lap to knock Andrea Dovizioso off the top spot at Motegi in Japan to head the times in a dramatic FP2, which saw Dani Pedrosa suffer a broken collarbone in a late spill.
Movistar Yamaha rider Lorenzo set a time of 1m 45.151s on his factory M1 with one minute remaining on the clock to take over from Italian rider Dovizioso, who had earlier led the way in opening free practice on the Desmosedici GP16.
Dovizioso was only 0.053 seconds behind the reigning champion in second place, with Maverick Vinales hot on his heels in third on the Ecstar Suzuki.
Young Spaniard Vinales impressed on the GSX-RR with a lap in 1m 45.248s, which put him in front of top Honda rider Marc Marquez, who slid out unhurt in FP2.
MotoGP World Championship leader Marquez saved a moment a Turn 1 but was unable to stay upright after gracefully sliding off at Turn 10.
However, his Repsol Honda team-mate Dani Pedrosa was not so lucky and was involved in a huge high-side at Turn 11 in the closing minutes. Pedrosa was taken to the medical centre for examination and it was later revealed that he had sustained a broken right collarbone.
British rider Cal Crutchlow slotted into fifth on the LCR Honda behind Marquez, 0.350s down on Lorenzo, while Aleix Espargaro on the second of the Ecstar Suzuki machines completed the top six.
Valentino Rossi, who lies second in the championship standings heading into the final four races, was seventh fastest with a lap in 1m 45.532s. The Italian rider was 0.381 seconds adrift of team-mate Lorenzo's benchmark time in FP2, but only three hundredths of a second off Crutchlow in fifth.
Pramac Ducati's Danilo Petrucci was next up in eighth ahead of the unfortunate Pedrosa, who took ninth in the session following his big off on the Repsol Honda.
Pol Espargaro, who was among the fallers, rounded out the top 10 on the Monster Tech 3 Yamaha (1m 46.245s).
Ireland's Eugene Laverty also came off after a big high-side on the Aspar Ducati. After being stretchered away, Laverty was able to walk unaided into the medical centre.
Aussie Jack Miller, making his return from injury on the Marc VDS Honda, was another rider who slid out in the final minutes.
Aprilia duo Stefan Bradl and Alvaro Bautista were 11th and 12th respectively ahead of Laverty, with Hector Barbera in 14th place on the second of the factory Ducati GP16s. Avintia Racing rider Barbera has been handed the opportunity to replace Andrea Iannone at Motegi, who is still not ready to make his comeback from injury.
Laverty's team-mate Yonny Hernandez finished 15th ahead of Britain's Scott Redding (Pramac Ducati), with Yamaha test rider Katsuyuki Nakasuga ending FP2 in 17th on the factory Yamalube Yamaha M1.
Bradley Smith, also back in action this weekend following an injury lay-off, was 21st on the Monster Tech 3 Yamaha behind Australian Miller and his team-mate Tito Rabat, plus Frenchman Loris Baz (Avintia Racing) in 20th.
1. Jorge Lorenzo
2. Andrea Dovizioso
3. Maverick Viñales
4. Marc Marquez
5. Cal Crutchlow
6. Aleix Espargaro
7. Valentino Rossi
8. Danilo Petrucci
9. Dani Pedrosa
10. Pol Espargaro
11. Stefan Bradl
12. Alvaro Bautista
13. Eugene Laverty
14. Hector Barbera
15. Yonny Hernandez
16. Scott Redding
17. Katsuyuki Nakasuga
18. Jack Miller
19. Tito Rabat
20. Loris Baz
21. Bradley Smith
22. Mike Jones
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