In a frantic and crash-interrupted session, the Australian beat Spanish team mate Dani Pedrosa into second place on the grid and prevented MotoGP leader Jorge Lorenzo from grabbing a hat-trick of poles.

The Spaniard, champion in 2010, was the fastest in the season-opener in Qatar and last weekend in Jerez.

Stoner's best lap of one minute 37.188 was 0.013 seconds quicker than Pedrosa's and teed the Australian up to gain the upper hand in the championship on Sunday.

Lorenzo has 45 points to Stoner's 41 with Pedrosa on 36.

Lorenzo led for most of the session until a red flag 11 minutes from the end forced a re-start. He finished fourth, his first time off the front row at Estoril since 2008, and behind third-placed British rider Cal Crutchlow on a non-factory Yamaha.

"The main problem for me today was that in turn one and two I couldn't enter aggressively so I lost a lot of time in this section," said Lorenzo, who shares the second row with American teammate Ben Spies and Spaniard Alvaro Bautista on a Honda.

"In general the bike is not giving me a good feeling so this lap time was the maximum I could get today...tomorrow is going to be hard as I have to try to pass Cal who is a hard braker." Crutchlow's time secured his second front row start in three races.

"The team have done a great job and I think we have shown our pace again," Crutchlow told BBC television. "It will be very difficult to be on the podium because Lorenzo is the fastest here, even though he is not on the front row, but we will see."

The red flag came out when Frenchman Randy De Puniet fell from his Aspar Aprilia and took out American Colin Edwards on a Suter-BMW. Edwards landed on his shoulder and was taken away on a stretcher with a fractured collarbone, similar to the injury he suffered last year.

Ducati's Italian great Valentino Rossi starts ninth.

Spaniard Marc Marquez took pole for the Moto2 race with Germany's Sandro Cortese quickest in Moto3.