The 31-year-old delivered his best flying lap when he switched to the softer 'medium' compound Pirelli tyres in the closing minutes of an hour's action that concluded with Lewis Hamilton suffering a major failure with his Mercedes car.
Alonso clocked a best time of one minute and 33.247 seconds that left his rivals trailing.
Championship leading defending triple world champion German Sebastian Vettel was one-tenth of a second slower in second place ahead of his Red Bull team-mate Australian Mark Webber, third by just 0.003 of a second.
Finn Kimi Raikkonen, champion in 2007, was fourth fastest for Lotus ahead of Hamilton, Frenchman Romain Grosjean in the second Lotus and German Adrian Sutil and his Force India team-mate Paul di Resta.
Hamilton's Mercedes team-mate Nico Rosberg was ninth and German Nico Hulkenberg 10th for Sauber ahead of Brazilian Felipe Massa in the second Ferrari and Briton Jenson Button in the leading McLaren.
Biggest drama
The top 12 were separated by less than a second and the top nine by just half a second.
Alonso survived a spin off the track with 20 minutes remaining before he led the move from 'hard' compound tyres to the softer versions and snatched pole.
But the biggest drama came after the chequered flag when the 2008 champion Hamilton suffered a rear suspension failure on the straight.
His left rear wheel appeared to sink and as it fell towards the asphalt of the circuit surface the tyre shed all of its outer shell of tread block rubber, leaving him to nurse his damaged vehicle towards safety.
"I've had a failure," he told the team by radio. "The left rear has gone."
Mechanics from the team then ran from their pits garage to recover the vehicle as Hamilton climbed out unhurt. – Sapa-AFP