The two-time world champion from Spain set the pace with a lap of 1 minute, 21.962 seconds for his 19th career pole. It was the Italian team's first qualifying win since the 2008 Brazilian GP -- a span of 30 races.
"It was a nice surprise," Alonso said. "A much better feeling. This was a great achievement by the team -- we proved that we were quick."
Defending world champion Jenson Button , of McLaren, finished just over one-tenth of a second slower to start on the front row for the first time in 23 races. Alonso and Button need strong showings in today's 53-lap race to stay close in the championship fight.
Felipe Massa , of Ferrari, and Mark Webber, of Red Bull, fill out the second row, while F1 leader Lewis Hamilton , of McLaren, will start fifth.
Sebastian Vettel was sixth for Red Bull, which had taken pole in 12 of the first 13 races this season.
Alonso, who crashed out of the Belgian GP two weeks ago, gave himself the best shot at moving up the standings with an electrifying run.
Hamilton, the 2008 F1 champion, has 182 points to lead Webber by three. Vettel is third with 151 points, and faces a difficult task today after his worst qualifying performance of the season. Button is next with 147 points, six more than Alonso.
ROLEX SPORTS CAR SERIES: In Tooele, Utah, Scott Pruett teamed with Memo Rojas to win the series' season-ending Utah 250 at Miller Motorsports Park, the Daytona Prototype championship duo's record ninth victory of the season
Pruett, driving a BMW-powered Riley Daytona Prototype, led the final 39 laps on the 3.048-mile, 15-turn road course. The Chip Ganassi Racing with Felix Sabates entry finished 1.946 seconds ahead of 2009 race winners Alex Gurney and Jon Fogarty .
The 50-year-old Pruett finished the season with an unprecedented third Daytona Prototype title, while Rojas earned his second championship.
Rojas, who qualified on the pole, led the first of 86 laps before being passed by Ricky Taylor . Rojas then turned the car over to Pruett, who beat Gurney and Taylor's co-driver, Max Angelelli, off pit road at Lap 48 and built leads of up to 8 seconds.
Angelelli was third, followed by Mark Wilkins and Ryan Dalziel.