Ducati's Valentino Rossi will start Sunday's Indianapolis round from just eleventh on the grid and behind the privateer CRT machine of Randy de Puniet.
The Italian lapped 1.950s from Repsol Honda pole sitter Dani Pedrosa and 0.326s behind de Puniet's Superbike-based Aprilia.
“It's a shame because this morning went pretty well,” said Rossi, who will return to Yamaha next season. “I was able to do some good laps both with the hard tyre and the soft, and in the end I wasn't so far off [in eighth place], actually lapping on the pace of the second group.
“That made me optimistic, and I thought that I could go 1'39” in qualifying, but I wasn't even able to match my time from free practice. I didn't have rear grip, and the rear tyre was sliding a lot.
“On the last fast lap, I had a big risk in the same turn where Nicky crashed. This track has strange asphalt that has less grip than what we're used to but that still wears the tyres. For that reason, we have tyres with stiffer carcases at our disposition here.
“We'll try to make some changes for tomorrow in order to gain a bit more grip, and we'll see what my race pace is.”
Hayden qualified as the top Ducati in eighth despite being one of three riders to suffer a big accident at Turn 13. However the American has been declared unfit to race.
The satellite Ducatis of Karel Abraham (Cardion AB) and Toni Elias (Pramac) qualified 14th and 17th.