The Factory Yamaha team, which won the 2010 MotoGP title with Jorge Lorenzo at Sepang, will start this year's Malaysian Grand Prix from the last two places on the grid.
A battered and bruised Ben Spies managed only 16th after falling in both of Saturday's sessions, while Lorenzo's injury replacement Katsuyuki Nakasuga will start his first MotoGP race from 17th and last.
“It's been a pretty eventful weekend. The bike is working really well but I'm just not feeling 100% and ready to get it over and done with," confessed Spies. "Qualifying was tough, we went out there and experienced a crash, I'm not sure why yet but we'll check the data later."
Spies' priority for race day is to protect his 17-point lead over Gresini Honda's Marco Simoncelli for fifth in the championship. Simoncelli has qualified in fifth place for the penultimate round of the year.
"We don't have a great position on the grid but we'll do the best we can for points to try and hold on to fifth place for the Championship," said Spies.
However, team director Massimo Meregalli revealed that Spies could yet withdraw from the grand prix.
“Ben is trying very hard; he's putting in all he can. We have to consider what is best for him tomorrow, so we will have a meeting tonight and make a decision for the race," he said.
4.1490sec off the pace on Friday, Nakasuga upped his game on Saturday to conclude qualifying with a best time 2.610sec from pole sitter Dani Pedrosa (Honda).
“This morning's session was quite positive for me. I had a good feeling and found a rhythm on the track which was very motivating," said Nakasuga. "Tomorrow I will try my best for a good position. The bike set up is working well so I am feeling confident for my first ever MotoGP race.”
Lorenzo's team manager Wilco Zeelenberg highlighted the contrast with last season.
“This is a completely different experience to last year where we won the Championship here. Now we are second last and last on the grid," he said.
"I think Nakasuga-san did a good job today, his lap time was a lot better than yesterday and he didn't crash so he did well."