Stoner, who will make now his final grand prix appearance in the Valencia season finale on November 9-11, also offered his congratulations to Lorenzo and condolences to Pedrosa.
"My biggest congratulations to Jorge, he's ridden an almost perfect season finishing 1st or 2nd when possible and I'm just disappointed not to be in the championship fight, but I made my own mistakes and this is how things go," he said.
"My condolences to Dani - I saw him crash out in front of me - but he had to push today and go out and win the race to keep his championship hopes alive. It was a small mistake, easy to do in that corner and I feel very sorry for him."
Now certain to finish third in the standings, Stoner has won five races this year and a sixth would put him equal for the season with Lorenzo and Pedrosa.