Australia's Casey Stoner will start Sunday's Portuguese MotoGP from pole position, despite leaving it late to record the best qualifying lap.
Repsol Honda's Stoner clocked one minute, 37.188 seconds to narrowly pip Spain's Dani Pedrosa.
Britain's Cal Crutchlow completes the front row, ahead of Jorge Lorenzo, Ben Spies and Alvaro Bautista on row two.
There was bad news for Colin Edwards, though, as the American broke his collarbone in a high-speed crash.
Edwards collided with Randy de Puniet of France within less than 12 minutes of the session remaining.
While De Puniet walked away and is expected to be fine for Sunday's race, Edwards was not so fortunate, breaking his collarbone for the second time in a year.
American Spies was a little unlucky, twice hitting traffic despite being on-pace to set a pole-challenging time, and had to settle for fifth place on the grid.
Andrea Dovisioso was seventh fastest on his Tech 3 Yamaha while Hector Barbera finished as the fastest Ducati in eighth.
Valentino Rossi came ninth while Nicky Hayden rounded out the top-10 fastest riders.
Crutchlow had looked on course for pole at one stage, before Stoner made his surge to the top.
"I am pleased because the team have done a great job and I think we shave shown our pace again," Crutchlow said.
"It will be very difficult to be on the podium because [Jorge]) Lorenzo is the fastest here, even though he is not on the front row, but we will see."
Marc Murquez will start on pole in Moto2 after recording a time of 1:40.934, with Britain's Scott Redding qualifying third and Bradley Smith 13th.
In Moto3, Sandro Cortese secured his second pole position of the season.
The 22-year-old German clocked a time of a 1:47.145 to finish more than three-tenths clear of Spain's Maverick Vinales.
Miguel Oliveira claimed third late in the session while Britain's Danny Kent, Cortese's team-mate, will start from fourth on the grid following his best qualifying performance of his career.
Selected MotoGP qualifying times from Estoril:
1 Casey Stoner (AUS) Honda 1min 37.188 secs
2 Dani Pedrosa (SPA) Honda 1:37.201
3 Cal Crutchlow (GBR) Yamaha 1:37.289
4 Jorge Lorenzo (SPA) Yamaha 1:37.466
5 Ben Spies (USA) Yamaha 1:37.723
6 Alvaro Bautista (SPA) Honda 1:37.917
7 Andrea Dovizioso (ITA) Yamaha 1:37.943
8 Hector Barbera (SPA) Ducati 1:38.006
9 Valentino Rossi (ITA) Ducati 1:38.059
10 Nicky Hayden (USA) Ducati 1:38.253