Jorge Lorenzo said his Motegi win came as a big surprise as he had been so far off the lead pace at Losail just a fortnight earlier.
Although the Yamaha number two had finished third in Qatar, he had been disappointed by the 16-second gap to winner Casey Stoner.
He was more optimistic after taking third on the grid following the qualifying wash-out in Japan, but did not anticipate being able to battle past team leader Valentino Rossi and secure his second career win.
"I didn't expect this victory," Lorenzo told the BBC. "It's true, I did not expect to win - because in Qatar I finished so, so far behind Stoner.
"Things were becoming better at this track, but not that much better that I thought I would win. I tried the best I could, rode well, and I was tired but I kept pushing because I wanted to win and have this opportunity."
He said it had a been an extremely tough race, as he made life harder with a poor start and then had to win a long dice with his world champion team-mate.
"It has been a difficult race, because I didn't do a very good start," Lorenzo said in the post-race press conference.
"I finished the first lap in fourth, I think. But after I caught up to the pace, I passed Valentino, I opened a little gap - one and a half seconds. He was pushing me very hard, so I had to ride as well as I could to get the victory."
The result gives Lorenzo a one-point lead over Rossi in the championship after two out of 17 rounds, with Stoner a further two points behind.
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