Jorge Lorenzo said second was the best he could achieve at Motegi as an inspired Dani Pedrosa was in control from the front.
Despite Motegi suiting the Hondas more than Lorenzo's Yamaha, the Spaniard had qualified second and had his race prospects boosted when Casey Stoner ran wide and lost the lead in the early stages.
Lorenzo said he had been hoping to further enhance his advantage by challenging for victory, but simply wasn't able to match Pedrosa's pace.
"I thought it was possible to fight with Dani, but he came better and better," Lorenzo said.
"Normally he struggles more than me in the late stages but he was inspired today and at a very high level of riding. He decided the victory and I couldn't follow him.
"I didn't expect such a strange race. I think one of the keys was the start, when I lost position and then Valentino [Rossi] almost took me off and I lost touch with Stoner. Then he went out, and Andrea [Dovizioso] had to go into the pits.
"I pushed to reduce the gap then to Dani but I couldn't - he deserved victory."
While Lorenzo was able to stay upright following contact with Rossi, his team-mate Ben Spies was less fortunate and was collected in the incident, dropping his bike into the gravel and falling to the back of the field.
He was able to rejoin and fought back to finish sixth, a fantastic return given the illness problems which dogged the start to his weekend.
"It was a bitter sweet race for sure," Spies said. "I really think if we had clear track and started well we could have been in 46s all race long and battled for the podium.
"I was in a perfect position coming out of turn three, right behind Dovi when I was hit from the back. I lost one hand off the handlebar and didn't have much control going into the gravel trap.
"That's racing, it sucks but there you go. I'm not going to blame anybody it's just a shame, we'll move on."