Stoner claimed pole position in impressive style.
Casey Stoner took pole position for the 2011 Qatar Grand Prix after setting the fastest lap of the weekend.
He blew all of the other riders away, including Dani Pedrosa, who will start second, and Jorge Lorenzo, who qualified third.
This was an impressive performance from the Honda riders, who outperformed the other teams throughout the session.
Lorenzo and Stoner traded places during the first few minutes, while Randy de Puniet elevated himself to third after seven minutes.
Pedrosa quickly replaced the Frenchman in third, while his teammate, Stoner, took the next opportunity to go even further ahead with a 1:55.186, with Lorenzo unsuccessfully attempting to dethrone him.
Dovizioso moved up to claim the third place on the front row after nine minutes, followed by Spies beating his old teammate to take fourth place.
Casey Stoner continued to eat away at his time, setting a new fastest lap after 11 minutes of qualifying. Dovizioso and de Puniet traded places before Aoyama claimed third place.
Spies moved into third position with 12 minutes gone in the session, just slightly slower than his teammate who pulled into the pit lane a few minutes previously.
Dovizioso continued to move to third before Pedrosa pushed his teammate and Lorenzo down as he took second place, while Spies moved to third.
After a lull in the action at the front of the field, Casey Stoner finally broke the 1:55 barrier with a 1:54.841, while Colin Edwards moved to sixth and Ben Spies went up to second place with half an hour to go.
Valentino Rossi moved up to ninth and Cal Crutchlow moved up to fifth with 20 minutes to go, before Aoyama managed to beat the British rider.
Colin Edwards regained fourth position as Dani Pedrosa set the fastest lap of the weekend after just under 20 minutes, while Ben Spies moved to third place.
With one quarter of the session remaining, Casey Stoner looked on course to displace Pedrosa at the top of the leaderboard, and he duly took first position on the grid with 1:54.375.
Meanwhile, Lorenzo moved up to third, seven-tenths behind Stoner with 12 minutes to go, as the majority of the riders made the long journey into the pits to get fresh tires with just over 10 minutes to go.
Ben Spies set his fastest lap as he grabbed fourth position with seven minutes to go, while Nicky Hayden stayed in 13th position.
Cal Crutchlow moved into sixth position, as Stoner moved further ahead at the top and Dani Pedrosa improved but still stayed second after a poor third sector.
Dovizioso moved into sixth place, while, de Puniet moved to 10th, Rossi moved into ninth and Simoncelli set a lap that left him fourth place.
However, as more riders came onto the track with two minutes to go, there was traffic throughout the track, ruining the laps of several participants.
Rossi and Simoncelli were both on course to set laps but were interrupted by other riders.
Dani Pedrosa attempted to get closer to his teammate on his last lap but stayed second, while Hayden moved 13th.
Pedrosa qualified second, while Lorenzo finished third, Simoncelli finished fourth, Spies fifth, Barbera sixth, Dovizioso seventh, Crutchlow eighth, Rossi ninth and Edwards 10th.
Randy de Puniet qualified 11th, Aoyama 12th, Hayden 13th, Capirossi 14th, Abraham 15th and Elias 16th.