The 28-year-old Frenchman had trailed Will Power after Friday qualifying, but left the Australian in little doubt as to who was the quickest man around the circuit as he lapped in 1:12.821 in his Newman/Haas/Langian Racing car.
His lap, which was 0.373 seconds quicker than anybody else, came on soft, red-walled Bridgestone tyres and saw him win the 27th pole of his career.
Dutchman Robert Doornbos, who had not taken part in the Friday session, was second quickest for Minardi USA, but will only start the race third after Team Australia driver Power guaranteed himself a front-row slot with provisional pole on Friday.
Perera ends Sebring test on top
05/02/2008 AT 16:19
Bruno Junqueira hung on to fourth place to give Dale Coyne Racing their best grid spot of the season while behind him Britain's Justin Wilson did well in his RuSPORT car to improve from 11th overnight to fifth on the grid.
Canadian duo Alex Tagliani and Paul Tracy were next up for Rocketsports and RuSPORT while French rookie Simon Pagenaud completed the fourth row for Team Australia.
Ninth and tenth were Neel Jani for PKV and Oriol Servia for Forsythe while Jan Heylen, who did not take part in Friday qualifying after his car was destroyed by Dan Clarke in practice, was 11th in front of his home crowd for Conquest.
British duo Katherine Legge and Ryan Dalziel both fell to 14th and 16th places respectively in their Dale Coyne and Pacific Coast cars.
Season 2008
Perera ends Sebring test on top
05/02/2008 AT 16:14
Conquest to double ChampCar assault
03/01/2008 AT 14:20