NASCAR spokesman Ramsey Poston said Montoya's fast lap was disqualified because a postqualifying inspection discovered his rear shock absorbers exceeded the maximum gas pressure allowed.
That moved two-time reigning Cup champion Jimmie Johnson up to the pole, with Montoya's No. 42 Chip Ganassi Racing Dodge moved to 42nd in the 43-car field for Sunday's race at Kansas Speedway.
It was a blow to Montoya, 24th in the season points and struggling most of the year to be competitive.
A team spokesperson said Ganassi officials were "evaluating the situation" and would have no comment until Saturday.
Before NASCAR's announcement, a delighted Montoya said, "It's huge. There's times where it's getting darker and cooling down and you run at the end and all of a sudden you pick up a half a second and you're up there. But we were in the middle of the pack and the track didn't really change that much. We were genuinely fast."
But, with his lap of 172.150 mph disallowed, Johnson's 172.007 gave him his fifth pole of the season and 18th of his career.
Matt Kenseth, another of the Chasers, moved up to third, but none of the other 10 were able to break into the top 10 and six of the contenders wound up 27th or worse.
"It was a very, very good effort for us," Johnson said before finding out he was on the pole.
"Everybody knows how important track position is. I thought that the 18 (Kyle Busch), the 99 (Carl Edwards) and the 31 (Jeff Burton), I thought some of those guys were much stronger than they posted today in qualifying. I thought they were better than that in practice. I was shocked to see some of those guys on the right side of the (timing) screen and at the bottom of it.
"But this is just one day of three and the important day is Sunday. It doesn't mean it's a layup weekend where we pick up points on the other Chase competitors, but every little bit helps."
Among the Chase competitors, after Montoya's disqualification, Dale Earnhardt Jr. was 11th, an ailing Jeff Gordon qualified 13th, Greg Biffle, winner of the first two events of the 10-race Chase, was 18th and Clint Bowyer 24th.
The disappointments were Busch in 27th, Denny Hamlin 30th, Edwards 36th, Kevin Harvick 38th, Burton 39th and Tony Stewart 41st.
Biffle was just one of a number of unhappy drives after his qualifying run on the slick 1.5-mile oval.
"We were hoping for a little bit better that that," said Biffle, teammate of Kenseth, Edwards, 13th-place David Ragan and 17th-place Jamie McMurray at Roush Fenway Racing. "We've just got something wrong with our cars here, all of us do, the whole group. I guess we've got one more day to figure it out."
The disappointed Stewart, seventh in the standings and hoping push his way into contention with eight races left in the Chase, couldn't explain his poor qualifying effort.
"We've been decent here," he said. "We've been decent all the way up until that qualifying run right there. I don't know what happened there. Something must have happened. We were decent in practice this morning, for sure."
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