The Spaniard overtook Jorge Lorenzo three laps later, while Rossi crashed out of the race, and reclaimed eighth place. He gradually started to up his pace as his confidence grew at the very wet Motegi track, but soon realised Aleix Espargaró, riding directly in front of him, was too far ahead.
In the second half of the race Viñales focused his attention on defending his eighth place from Lorenzo, who arrived at the back of his Yamaha with six laps to go. The number-25 rider put his head down, but was unable to hold off his compatriot. He crossed the line in ninth place, 36.575s from the front.
Rossi also had a good launch off the line, starting from 12th on the grid. He quickly began his charge and had picked up three positions by the end of the first three laps. The Doctor spurred on his YZR-M1 to prevent his rivals from clearing off at the front, overtaking Lorenzo on lap 6. However, his pursuit came to a premature halt when he suffered a crash in turn 8 and was unable to rejoin the race. Today's race results see Viñales and Rossi hold third and fifth place respectively in the championship with a 41 and 76 point-gap to the leader. Yamaha is in third place in the Constructor classification, 29 points from first, and Movistar Yamaha MotoGP is chasing the Team title in second place with 43 points to the top of the rankings.
The team will soon head south to take part in next week's Michelin Australian Motorcycle Grand Prix on Phillip Island, Australia.
"I expected things to be a little bit worse, because this morning I was trying to be in the top-15. Finally, in the race, I pushed a lot in the beginning. I tried to risk only the necessary, trying to give our best. Today this was the maximum and we will have to think now about Australia. Until all the points are collected it is impossible to know if there is still a chance to win the championship. For sure we we'll face different circumstances in Australia. It will be a different bike and different tyres, we don't know what we're going to have there, but it's a track I like a lot, I like to ride there, so I can't wait to be on the bike again."
"Today was the end of a very difficult weekend. Because of the wet conditions I was not very competitive, I was struggling a lot with the wet setting of the bike. In the race I was trying to follow Aleix Espargaró and I was trying to stick with him, but unfortunately I crashed. Now we'll try to do some good races and it will be important during the next weekends to give Yamaha as much information as possible to improve the bike and to decide on the direction for next year."
"When we arrived here in Japan, we weren't expecting this weekend to be as difficult as it turned out to be. We really worked hard to try to find a solution. We put in a lot of effort, but we weren't able to do it in the end. We never found the rear grip that the riders were looking for in almost all the sessions, as well as in the race itself, but Maverick and Valentino tried to make the best of it. We know that we have a lot of work ahead of us, and I expect that we will use the next round to explore different solutions for the future."