Marco Simoncelli held pole position at Estoril from the 12th to 55th minute of the hour, at which point reigning world champion Jorge Lorenzo edged ahead by 0.133sec.
Simoncelli should have then had several laps to respond, but any hopes of a debut MotoGP pole disappeared when he fell from his San Carlo Honda Gresini bike.
Fortunately for the Italian, who also crashed out of the race lead last time at Jerez, he had done enough to secure his best MotoGP start of second and believes he can fight for victory - or at least a debut rostrum - on Sunday.
“There's a bit of disappointment and there's no use hiding it because after dominating the two sessions yesterday and then this afternoon the pole position was in my hands,” confessed Simoncelli. “Unfortunately I made a little mistake which prevented me from improving my fastest lap.
“Anyway, turning our attention to the race I have to be happy because my race pace is quick and I am confident with the bike even though we have a little problem with the front. The front tyre available to us is a little soft for us and moves around a lot so maybe a harder option would have been better.
“We have improved the grip on the rear so I think tomorrow we can be fighting for the win if not the podium. To be annoyed at not being on pole position is not a bad thing. Tomorrow will be a tough race but I'm ready to fight and give my all. ”
After qualifying Simoncelli had a public disagreement with reigning world champion Lorenzo in the press conference, over comments Lorenzo had made about Simoncelli being a dangerous rider.
Simoncelli said he felt Lorenzo was wrong, while remaining relaxed and making jokes. Lorenzo also stuck to his guns, but insisted it was a serious matter...