The session was interrupted five times by red flags, Max Verstappen among those to be caught out as he qualified only 12th
The rain that postponed qualifying on Saturday had eased overnight, though remained in the area and threatened to worsen as the session progressed.
That prompted most to head out immediately as the proceedings began with the full wet tyres the order of the day.
Unsurprisingly, it was slippery, with Liam Lawson, Zhou Guanyu, and Lance Stroll sliding off the road in the final sector.
Esteban Ocon was confident early, the Frenchman fastest from the off with a 1:30.096s.
Setting a time wasn’t trivial, however.
In addition to the slippery surface, the steady stream of yellow flags saw a host of laps deleted for drivers who happened to be at the wrong place at the wrong time.
Track limits were also an issue, especially at Turn 4 – the left-hander off the back straight.
With nine minutes remaining, the session was stopped for Franco Colapinto, who crashed a Turn 3.
The Argentinian quickly confirmed he was okay to the team but remained in the car for a time.
Under the stoppage, Yuki Tsunoda sat atop the timesheets from Charles Leclerc, while Max Verstappen was seventh and Lando Norris 10th.
Both Oscar Piastri and Lawson were inside the top 15, too; the drivers in danger were Albon, Zhou, George Russell, Lewis Hamilton, and Valtteri Bottas.
At the restart, the Finn reverted to the full wet tyres, having gambled with the inters earlier on, as the rain intensified.
Oliver Bearman had initially planned to head out on inters, but pulled out of the queue at pit exit to swap back onto the full wets.
The initial laps saw a smattering of personal bests as they cleared the racing line once again.
As that process continued, several drivers improved, pushing Lawson into the bottom five, just over two tenths away from the cut-off to progress to Q2.
Having sat 20th with three minutes remaining, Russell went second best despite being caught behind Stroll on the run to the line.
Inside the final minute, Hamilton was only 17th with time for just one more lap.
Lawson was in the same boat, the Kiwi having had a time deleted for yellow flags when Nico Hulkenberg skated off the road ahead of him.
Hamilton improved to 14th, pushing Norris into the bottom five.
He delivered, but only barely, rising to 15th as he completed his lap.
Lawson also escaped, just one place ahead of the McLaren, Hamilton pushed back into the bottom five along with Bearman, Colapinto, Hulkenberg, and Zhou.
At the other end of the timesheets, Verstappen went fastest with his final lap, a 1:28.522s to head the segment from Albon, Russell, and Ocon.
The weather eased ahead of Qualifying 2, tempting Piastri out onto intermediate tyres.
He was the only driver to brave the shallowed groove rubber initially.
Sainz opened proceedings with a 1:29.406s on the full wets, suggesting track conditions had not improved significantly, if at all, from Q1.
From there, times did begin to tumble with Perez logging a 1:28.158s to suggest the crossover to inters was closing.
On his first lap, Piastri was around a second off that pace, though an encouraging time given his lack of experience (and confidence) on the tyre.
Next time around, he was fastest of anyone and shot to the top of the timesheets by six-tenths – a 1:27.141s.
That prompted a sea change with the field heading to the pits for a set of intermediate tyres with eight minutes remaining in Qualifying 2.
Still on track, Piastri was going faster, clocking a 1:25.179s, a lap 2.6s faster than second-fastest Verstappen.
Moments after Russell completed his lap, a 1:26.307s, the red flags were shown for a second time.
This time it was for Sainz, who spun into the wall on the exit of Turn 2, heavily damaging the right-rear corner of the Ferrari.
The clock stopped with just under six minutes remaining, Piastri fastest from Russell, Stroll, Verstappen, and Lawson.
Norris meanwhile sat 11th and in the danger zone having yet to record a lap on the intermediate tyre.
He headed the queue as the session restarted eight minutes later, and was quickly on the pace, improving to third fastest straight out of the box.
Others were also improving, including Fernando Alonso who moved onto provisional pole – briefly – before Norris completed his second timed lap.
Moments later, and with less than a minute remaining, the third red flag was thrown again as Stroll was off the road at Turn 3, in a similar fashion to Colapinto earlier.
It caught both Verstappen and Perez, the pair in 12th and 13th, along with Bottas in 12th, Sainz, and Gasly.
With a five-place grid penalty, Verstappen will fall to 17th on the grid.
Norris meanwhile progressed fastest from Alonso, Piastri, and the impressive Lawson.
Stroll also progressed, though he would take no further part in the session.
Forecasts suggested rain would intensify in the latter stages of Qualifying 3, prompting a busy start for the nine surviving drivers.
Times were marginally slower than the end of Q2 but rapidly improved.
However, that was interrupted by another red flag, the medical car again deployed. This time after Alonso crashed towards the end of the lap.
The rear end got away from the Spaniard as he plunged down the hill at Turn 11 – Mergulho – where he collided heavily with the wall with the right-hand side of the car.
Seven minutes remained on the clock under the stoppage, with Norris fastest from Albon and Piastri, with Ocon, Russell, Leclerc, Tsunoda, Lawson, and Alonso.
During the stoppage, the forecast changed with no further rain expected.
Such was the desperation to get track position, and time on track, a queue formed at pit exit five minutes before the resumption.
It was brief, the session’s fifth red flag thrown as Albon crashed at Turn 1, the clock stopping with 3:31 remaining.
There was significant damage to the rear of the Williams, Albon quickly reporting that he was okay.
The rear of the car stepped out on approach to the first corner, pitching him into a spin and the barrier.
Norris remained atop the timesheet under the stoppage with Albon still second from Piastri.
Tsunoda had also had a moment, appearing to dip the outside wheels onto the grass on approach to Turn 4, though he managed to extricate the RB to remain in the session.
Again there was a rush to get back out on track, Ocon heading the queue from the two McLarens at pit exit with Leclerc fourth in line.
Norris was instructed to be sensible, with rain expected to return and the race only a matter of hours away.
Russell remained in the pits, opting for only a single flying lap at the end of the session.
Conditions were conducive to fast times, with personal bests and even session bests immediately out of the pits.
Norris improved his best, a 1:24.092s, while Piastri did not improve and then locked up into Turn 1 to scupper his chances of going faster on his final lap.
That saw him drop down the order as Russell went second fastest from Tsunoda, Ocon, Lawson, Leclerc, Albon (who didn’t run) Piastri, Alonso, and Stroll (who also didn’t run).
Norris had improved again on his final lap, lowering the benchmark to 1:23.405s to take pole by 0.17s over Russell while RB enjoyed a dream session with third and fifth on the grid, while constructors’ championship rivals Haas will start well down the order.
The rescheduled Sao Paulo Grand Prix begins at 12:30 local time (02:30 AEDT Monday).
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