Casey Stoner rued a handling problem at the rear of his Ducati after falling from pole position to third place at Catalunya.
The Australian was beaten off the line by second place starter Dani Pedrosa and rapidly fell back from the Honda rider, before losing the runner-up spot to Valentino Rossi following a long tussle.
"For some reason from the beginning of the first lap, my rear was all over the show," Stoner told BBC television.
"We were confident with the race set-up but as soon as we got into the turn I knew something was wrong."
The lack of race pace left the reigning champion extremely frustrated, as he had been confident of fighting for victory today.
"I just couldn't do anything more," said Stoner, who has not won since the Qatar season-opener.
"I found out how to ride around it by keeping the bike upright a little bit more, but we were still struggling so much.
"I'm really, really disappointed with this result because this is the only race we've been capable of winning and today there was no way it was impossible."
Although he re-passed Rossi in the middle of the race and held on to second place until the penultimate lap, Stoner admitted that he always suspected the Italian would beat him to second in the end.
"If we'd had pretty even machinery, there were places where I knew I could have passed him, but we just couldn't get any drive out of the corner and were just losing too much," Stoner said.
I was having to make it up on the brakes, but by the time I'd made it up, there was no more room to make an overtaking pass. I was fighting a losing battle really."