Jarno Trulli will start on pole in Bahrain with Timo Glock next to him as Toyota brilliantly locked out the front row for the first time in Formula 1.
Red Bull's Chinese Grand Prix winner Sebastian Vettel came through in third but team-mate Mark Webber was controversially knocked out early on.
The British pair of Brawn GP's Jenson Button and McLaren's Lewis Hamilton start in fourth and fifth respectively.
Embattled Ferrari showed improvement and are eighth and 10th on the grid.
Angry Webber was the biggest casualty of a dramatic qualifying session, finishing down in 19th after being blocked during a pacey lap late on by Force India's Adrian Sutil in the first knockout phase.
"It doesn't matter if I protest," the Australian told BBC Sport. "My race is screwed.
"I don't usually get caught out in traffic but it was the worst corner [the last] to get nailed on. An absolute disaster."
Sutil, who himself finished in 16th but has been handed a three-place grid penalty, admitted his mistake afterwards.
"It was a tricky incident," he said. "I saw Webber in my mirrors but I thought also he was on an out lap so I defended my position.
"There was a big confusion, I just didn't know what to do. I will go and apologise [to Webber] now."
Though they have been increasingly impressive since the first race in Australia, Toyota's achievement marks another surprise twist in an already-riveting season which some feared may be dominated by Brawn after Button romped to victory in the first two GPs of 2009. BBC Sport Report
Was a very good Qualifying session I must admit. Happy to see Hamilton nearer the top, and to see him fastest in Practice as well. Seeing his lap in Q1 was an absolute pleasure.. not the tidiest line, but shows you dont have to be boring to be fast.
Gutted for Webber though, had such promise for this race as well.