Jorge Lorenzo bolted clear for his fifth victory of the year in Sunday's San Marino MotoGP, at Misano.
Pole sitter Marc Marquez dropped to a low of fourth after an early braking mistake, then repassed Valentino Rossi and Dani Pedrosa.
Rossi dropped away from the Hondas in the second half, while Pedrosa and Marquez exchanged second place several times.
Marquez confirmed the runner-up spot in the closing laps, finishing 3.4s from Lorenzo, meaning Marquez's title lead has still grown from 30 to 34 points - but with Lorenzo and Pedrosa now tied for second.
Lorenzo and Rossi were using the factory's new seamless shift gearbox for the first time in a grand prix.
Aleix Espargaro, who had qualified on the second row, received a jump start penalty.
Ducati test rider Michele Pirro was again replacing the injured Ben Spies at Pramac.
for pictures from the grand prix...
1. Jorge Lorenzo
ESP Yamaha Factory Racing (YZR-M1) 44m 5.522s
2. Marc Marquez
ESP Repsol Honda Team (RC213V) 44m 8.901s
3. Dani Pedrosa
ESP Repsol Honda Team (RC213V) 44m 12.890s
4. Valentino Rossi
ITA Yamaha Factory Racing (YZR-M1) 44m 20.584s
5. Stefan Bradl
GER LCR Honda MotoGP (RC213V) 44m 27.877s
6. Cal Crutchlow
GBR Monster Yamaha Tech 3 (YZR-M1) 44m 28.121s
7. Alvaro Bautista
ESP Go&Fun Honda Gresini (RC213V) 44m 36.581s
8. Andrea Dovizioso
ITA Ducati Team (GP13) 44m 48.224s
9. Nicky Hayden
USA Ducati Team (GP13) 44m 50.380s
10. Michele Pirro
ITA Ignite Pramac Racing (GP13) 44m 53.340s
11. Bradley Smith
GBR Monster Yamaha Tech 3 (YZR-M1) 44m 53.533s
12. Colin Edwards
USA NGM Forward Racing (FTR-Kawasaki CRT)* 45m 8.676s
13. Aleix Espargaro
ESP Power Electronics Aspar (ART CRT) 45m 13.122s
14. Hiroshi Aoyama
JPN Avintia Blusens (FTR-Kawasaki CRT)* 45m 21.050s
15. Danilo Petrucci
ITA Came IodaRacing Project (Suter-BMW CRT)* 45m 23.429s
16. Claudio Corti
ITA NGM Forward Racing (FTR-Kawasaki CRT)* 45m 35.177s
17. Randy De Puniet
FRA Power Electronics Aspar (ART CRT) 45m 39.512s
18. Michael Laverty
GBR Paul Bird Motorsport (PBM-ART CRT)* 45m 42.382s
AUS Go&Fun Honda Gresini (FTR-Honda CRT) DNF
ESP Avintia Blusens (FTR-Kawasaki CRT)* DNF
COL Paul Bird Motorsport (ART CRT) DNF
CZE Cardion AB Motoracing (ART CRT) DNF
ITA Energy T.I. Pramac Racing (GP13) DNF
CZE Came IodaRacing Project (Suter-BMW CRT)* DNF
* Standard ECU.
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