Lando Norris could qualify only third for the sprint race at the Qatar Grand Prix - on the weekend the McLaren driver could clinch the world title for the first time.
Norris' team-mate Oscar Piastri, one of his two championship rivals, took pole, with Mercedes' George Russell second.
Red Bull's Max Verstappen - tied with Piastri in the title race, 24 points behind Norris - had a difficult session and will line up sixth for the sprint.
Norris cannot win the title after the sprint on Saturday, but can in the grand prix on Sunday if he can gain two points on both Piastri and Verstappen.
Piastri had a smooth qualifying for the sprint, fastest on both his flying laps.
Norris, by contrast, damaged his floor with an off during the second session, but despite that was just hundredths behind Piastri on his first lap in the final session.
He then had his last lap compromised by running behind Williams' Alex Albon and was already off the pace before running wide out of the final corner, before an off-track moment out of the final corner on his second lap, and was pipped by Russell.
Piastri, who has seen Norris make up 50 points on him since he won the Dutch Grand Prix at the end of August said: "It's been a good day, which is nice for a change.
"The car has felt good all day. We made some good adjustments into qualifying. The pace was there all day."
Norris said: "The pace was there. I just made a mistake in the last corner on my first lap and didn't put it together.
"I'd be stupid to not try and win [the sprint race]. See what I can find overnight.
"It's impossible to overtake, so I think I am probably going to finish P3 but if I can at least get George off the line, that's probably the most I can hope for."
There are eight points for a win in the sprint, seven for second and so on, down to eighth place.
Verstappen unhappy; Hamilton virtually mute
Piastri's pole came despite a major oversteer moment on the entry to Turn Four, which he estimated had cost him about 0.2secs and he described as "pretty scary - turning left in a right-hand corner is never good, especially when you're doing however many hundreds of kilometres an hour you're doing there".
Underlying Verstappen's troubles, the Dutchman was beaten by his team-mate Yuki Tsunoda in qualifying for the first time this season, the Japanese faster by 0.009secs.
Verstappen was complaining, with added swear words, through the session over the radio about the car bouncing.
Despite that, he was fastest in the first session, and within 0.1secs of the McLaren drivers in the second. But he damaged his floor with an off at Turn Four on his first flying lap in the final session, compromising his car's performance.
It was the first time he had been out-qualified by a team-mate since the 2024 Azerbaijan Grand Prix.
Verstappen said: "Not good. From the first lap just really bad bouncing and very aggressive understeer that would switch into oversteer in high speed. Just not what you want. We tried to change a few things on the wheel but it never really worked.
"With this balance, in the sprint it will not be a lot of fun. It will be more about trying to survive and then make some changes going into qualifying."
Although overshadowed by the title fight, arguably the star of sprint qualifying was Fernando Alonso, who put the Aston Martin fourth on the grid - an outstanding performance for a team that lies eighth in the constructors' championship.
"One of the best results of the year," he said. "Tough circuit, high-speed sections and the car seemed in the window already in first practice. A bit of stress in Q2 because of traffic but we made it into Q3 and then we put a lap together.
"Twenty-four years' experience, 44 years old, it has some disadvantages. I get a bit more tired with the jet lag.
"But I know the tracks, the tyres, and know how to extract everything on Fridays, and then on Saturdays it's true we open parc ferme and make some small changes to the cars and everyone seems to get on top of the circuit."
Behind him, Mercedes' Kimi Antonelli was seventh, with the Williams of Carlos Sainz and Alex Albon sandwiching Leclerc.
Hamilton said almost nothing in his sole media interview after the session.
Asked how tricky the car was, he said: "Same as always."
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