Gresini rider Redding beat fellow production Honda racer Hayden’s Aspar bike over the line by three tenths of a second after a race-long dice.
But the Briton was adjudged to have “rejoined in such a way that he gained an advantage” when he went off the course at Turn 1 three laps from the end.
A time penalty was imposed to drop him behind Hayden in the results.
The Gresini team appealed, but race direction’s verdict was upheld by the FIM stewards.
Redding felt he had done enough to make up for what he had gained at Turn 1.
“I had a problem backshifting into Turn 1 and, rather than risk a crash, I opted to run on,” he said.
“I gained a little bit of time, but in sector two I slowed to make up for this.
“In the end I got penalised for the time I made up in Turn 1 and me slowing down in sector two wasn’t taken into account.
“It’s difficult to accept, because if I hadn’t slowed down to make things fair, even with the penalty I’d have finished 12th.
“Yes, I’m disappointed, but there’s nothing I can do about it, so we have to move on.”
Race winner Marc Marquez had a similar moment at Turn 1 earlier in the race while trying to take the lead from Valentino Rossi, but backed off as he rejoined the course to enjoy he slotted in behind both Rossi and Dani Pedrosa.