Yamaha team-mates and multiple world champions Jorge Lorenzo and Valentino Rossi will start just 12th and 15th respectively in Sunday's Australian MotoGP.
Already on the back foot after being left 19th and 20th in Friday's storm-shortened practice, the pair were again caught out by the fluctuating weather as they failed to break into the top ten during the extended FP3 session on Saturday morning.
That in turn forced them to battle the likes of Cal Crutchlow and Maverick Vinales in Qualifying 1, where just two transfer places were available for the following pole shootout.
While Lorenzo secured second to Crutchlow on his last lap, Rossi was down in fifth after making an ill-fated decision to switch from a wet to intermediate rear tyre on the drying track.
Track conditions continued to improve during Qualifying 2, but Lorenzo was left in last place, a massive 6.7s from pole sitter Marc Marquez.
The Repsol Honda rider, handed the world title when Rossi and Lorenzo both fell last Sunday in Japan, was surprised by their Phillip Island grid positions. But, like fellow front row starters Crutchlow and Pol Espargaro, he expects a strong fightback in the race.
"Jorge looks like he's struggling in these kind of [changeable] conditions, but in Qualifying 1 he did a good lap on wet tyres to go in to Qualifying 2. But then he was struggling again in Qualifying 2," Marquez said. "About Valentino, he stopped in the box to put the intermediate in Qualifying 1 but it was still not the correct time. He took the risk and this time it was not the correct strategy.
"You never know, maybe they will go out tomorrow and be the fastest because we know they have a lot of talent. I think tomorrow, if it is a normal race, they will be fast."
Despite their starting positions, Crutchlow admitted he'll probably be caught by at least one of the factory Yamahas during the race. But he also warned making up so many places is not easy at Phillip Island.
"It's a surprise sure, to see them so far back, but it can happen to anybody in the world," said the Englishman. "It could happen to Marc, Dani, Jorge anybody over the years. You have tricky conditions, the way they have been in the last days, and Jorge we know is not pushing very much in these conditions at the moment. And as Marc said, Vale just got caught out with the timing [of the tyre change].
"It's a shame for them, but I expect them to be there in the race. The only difficulty here is that there are not so many passing places in the first parts. It takes a bit of time for the race to string out and then you can start to push. But I wouldn't be surprised if I was passed by one of them in the race at some point. You never know with those two!"
Tech 3's Espargaro, the top Yamaha rider in qualifying, fears such a pass will come sooner rather than later.
"Everyone can struggle in one day. Today was not their day. For sure they are amazing riders," he said. "They were unlucky. It's happened to me many times in these conditions. I think it's my first time in this situation that we get a good result after three years in MotoGP! So it can happen. For sure tomorrow in the race they will be competitive again. I hope they overtake me late, but I think it will be soon!"
Yamaha has not won a MotoGP race since Catalunya in June.
By Peter McLaren