Driving a Ford/Lola, Bourdais averaged 101.076 miles per hour at Fundidora Park to improve five positions from Friday's provisional qualifying and will be joined on the front row by Canada's Paul Tracy.
Bourdais became the second driver in Champ Car series history to win poles in his first two starts, matching the 1993 feat of Nigel Mansell.
Tracy held the provisional pole at the 2.104-mile road course but crashed his Ford/Lola in Saturday's morning practice and did not turn a lap.
"I spun into the curbs this morning, damaged the bottom of the tub on my car, punched a hole through the bottom," said Tracy, who was guaranteed a spot on the front row and will use a backup car Sunday.
Bourdais also won the pole in his Champ Car debut last month in St. Petersburg, Fla.
"I really thank a lot to Newman/Haas Racing because I feel we did a great job this weekend," he said. "I just hope it will be like this all season long. We'll see tomorrow."
The 34-year-old Tracy won the season opener in Florida.
"We weren't able to repair the car," he said. "We would have had to have taken out the spare car for qualifying. That would delete our time from Friday. The only logical choice was to sit out."
Alex Tagliani of Canada will start third here for the second year in a row after he snatched the position from Spain's Oriol Servia on his final qualifying lap.
"It's just a good boost for everyone on this team," Tagliani said. "On the first set of tires, I had a problem on the back straightaway. Later on, we put on our second set."
The pole changed four times as Servia kept pushing his Ford/Lola before Bourdais sealed the spot. Servia was second-fastest Friday and will start fourth.
"The car was very good," Servia said. "I look forward to the race."
Local fans will keep a close eye on Mexicans Michel Jourdain Jr. and Adrian Fernandez, who qualified fifth and sixth.