The Repsol Honda rider had made a sluggish start from sixth on the grid and slipped to eleventh on the first lap, before staging a spirited comeback.
Hayden had front-running pace but while passing
Toni Elias for sixth, the American ran off track and dropped all the way back to tenth.
"Unfortunately I didn't get a great start and on the first lap or two I got boxed in everywhere and I always seemed to be in the wrong place at the wrong time," reflected Nicky. "That cost me a lot of positions but once things settled down I started moving forward and was going well. Then, passing Elias at the end of the back straight, I got in too hot and it was a silly mistake which I'm not happy about. I was in the draft and just got into the corner a little too fast.
"After that I got back on the track, put my head down and I'm actually proud of the way we recovered and started setting some really quick laps. First I caught Colin and lost a little time getting by him. Then I was able to catch Hopkins and Vermeulen on the last lap but we ran out of time to pass them," continued Hayden. "Our speed and rhythm was way better than ninth place today and that's encouraging, but it was rider error that cost us a better result today. We've got one more chance to get the job done in Valencia in two weeks."