The neutrals sent Rossi wide on numerous occasions and he had dropped to last place on lap 9 of 28.
Initially considering pulling out, Rossi not only went the distance - but had climbed back up the order to tenth at the chequered flag.
“Unfortunately, after some laps, I started having problems with the gear box," said Rossi. "When I shifted down, I remained in neutral. So I made two or three mistakes for this reason on the first corner. And I wanted to stop, seriously.
"But I try to not give up before I arrive at the end. I remained in neutral another two or three times and tried to take some points, but it was very, very sad.
"We know that we have to work hard. Ducati is doing that, and my team and I are as well, because we must try to not let up and to get the bike ready while we wait for technical updates.”
Rossi has now dropped from fourth to sixth in the world championship standings heading into his second home round of the season at Misano this coming weekend.
Team-mate Nicky Hayden made a pit stop on his way to 14th at Indy, having suffered major front tyre problems after chasing the softer option.
