Junqueira covered the 4.05-mile road course in 1 minute, 43.917 seconds for an average speed of 140.235 miles per hour. He was .805 seconds faster than Newman/Haas teammate Sebastien Bourdais of France.
"I didn't expect to be this fast," admitted Junqueira, who is trying to nail down his first pole of the season. "My first lap was a very good lap and I felt that was the best I could do. Then on my next run, I went two-tenths faster."
Bourdais' top lap was 139.157 mph, barely edging Paul Tracy for second heading into Saturday's final round of qualifying.
Adrian Fernandez of Mexico was fourth at 139.140 with Canada's Patrick Carpentier rounding out the top five.
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