The Briton had looked strong heading into the final Q3 shootout for the top grid spots, after leading the way in the Q2 segment of qualifying for Sunday's race.
But drivers endured a tricky time in setting their laps in Q3 as a major storm blew over the Interlagos track, and Norris failed to repeat his earlier form to end up seventh on the grid.
Max Verstappen claimed the top spot ahead of Charles Leclerc and the two Aston Martins.
Afterwards, Norris could not hide his disappointment at the missed opportunity.
"The car was amazing," he said. "It was quick enough to be quickest today and on pole, so pretty gutted [to end up] the way we did.
"I don't know what to feel about [it]. I think the car was amazing.
"It came alive a lot in qualifying and was easily good enough to be quickest, let's say. Delivering the lap, and putting it together in Q3, everything's a different job.
"Easily quick enough, so disappointed. Another disappointing Saturday, not a lot we could have done."
McLaren's misery at the lost opportunity of qualifying was compounded by Oscar Piastri making a mistake on his single Q3 run, as he slid off the track at the Juncao corner that leads back up to the start-finish straight.
Piastri said he had done nothing different to before on that lap, as a number of drivers said that grip levels had disappeared even though the rain had not hit.
"I just lost a lot of grip," said the Australian, who was unable to set a timed lap in Q3 and thus ended up 10th on the grid.
"I don't know if it was already raining or what, but I was struggling a lot already on the lap. I think everyone was.
"I just went in how I did the last lap and just slid straight off. So yeah, it's a shame. The pace of the car was looking good, but we try again tomorrow."
After electing not to show its full potential in the morning practice session, Piastri said that everything had looked well on course for McLaren in qualifying before the storm blew in.
"It's been a good day in terms of pace," he said. "Obviously this weather's thrown a spanner in the works, so we just need to look at what went wrong in Q3."
