Driving a Ford/Lola, Fernandez averaged 93.553 miles per hour around the 1.15-mile street course to score his fourth career pole and first the 2002 Monterrey GP.
Fernandez is looking for his second win of the season, having won the G.I. Joe's 200 in Portland, Ore., on June 22.
Miami resident Bruno Junqueira of Brazil, who won the provisional pole Friday, crashed his Ford-Cosworth/Lola between turns 3 and 4 and will start second. Junqueira also crashed in practice Friday prior to the qualifying session.
In last year's race, Junqueira started 10th and led 16 laps but finished fifth. He is second in the championship standings, 17 points behind Paul Tracy. Oriol Servia of Spain took third at 93.477 mph in a Ford/Lola.