The Spaniard, driving a Renault, set a new lap record with a time of 1 minute, 13.698 seconds to edge six-time world champion Michael Schumacher of Germany for the top spot.
"The car has been quick all weekend, and pole position gives me a solid base for Sunday's race," Alonso said. "I did a very good lap. The car was under-steering a bit too much at low speed, but it was very stable in the high-speed corners. I am happy to be on pole, but the main job is still to come."
Schumacher, who has won eight of the nine races this season, could not get within a quarter of a second of Alonso and ended the hour-long session 0.273 seconds slower than the Renault driver.
Scotland's David Coulthard produced his best qualifying effort of the season in McLaren's new car to offer hope for the future. Coulthard has only nine points in this season but claimed third place, just 0.289 seconds behind Alonso.
Swim Week Miami Beach 2014 [PHOTOS]