The 23-year-old Kaiser, the last driver to take the track, averaged 227.372 mph for his four laps, a mere 0.019 mph ahead of Alonso's 227.353 mph average in the McLaren-prepared Chevrolet.
"We never surrendered. We kept trying," Alonso, 37, told reporters after a tough week at the famed speedway.
The Spaniard crashed his Chevrolet in practice on Wednesday and missed nearly two full days of practice while a back-up car was prepared.
Then he tried five times on Saturday to qualify, puncturing a tyre on the first attempt.
Alonso had a completely new set up for Sunday's shootout but could not get the speed he needed to qualify.
"I think the car felt better today than what we had yesterday. (So I am) happy with things we tried," he told reporters before learning he had not qualified.
Pagenaud had a four-lap average speed of 229.992 mph to become the first Frenchman to take the pole since Rene Thomas in 1919.
“It’s just amazing,” Pagenaud, who last week won the IndyCar Grand Prix on the track’s road course, told NBC Sports. “Obviously last week was amazing, but this is even more special.”
He will be joined by Ed Carpenter (229.889) and Spencer Pigot (229.826) on the front row.
But the Cinderella story belonged to Kaiser, the 33rd qualifier.
“I don’t think I can wrap my mind around what we just did,” he said after bumping Alonso from the field.
“This is all the credit to the team. They’ve been working non-stop trying to get this car ready for us and they did everything that we needed to get into this field.”
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Ken Ferris)
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