The Canadian, who is fighting for a new contract to remain on the grid with the Grove team, surprisingly bolted to the top in the dying moments of a slippery FP3 to pip second practice pacesetter Leclerc.
Alex Albon, who had taken the flag moments before his Williams team-mate, secured third ahead of his former Red Bull stablemate and defending champion Max Verstappen.
A downpour in the hour leading up to FP3, which helped flood the paddock and caused a few motorhomes to leak, created a cautious start to the hour-long Saturday session.
Leclerc was the first car to emerge after three minutes, followed shortly by team-mate Sainz and then both McLarens, Zhou Guanyu's Alfa Romeo, Lance Stroll and Mick Schumacher joined the action.
The full wet tyre was the pick of the bunch, Leclerc taking the blue-walled rubber to a 1m46.044s initially before Sainz found half a second to sit provisionally top of the pack.
Then two-time champion Alonso ventured out on intermediates, requiring plenty of corrections throughout the lap and he was ultimately 5.8s off the pace as the crossover point was yet to arrive.
The full wets continued as the optimal tyre for the conditions, as Leclerc only needed 10 mins to post his 1m43.364s effort that would take him to the head of the leaderboard for almost the entire session.
That offered him a 1.25s cushion over Sainz before heavier rain arrived - with none of the Red Bull or Mercedes cars having left the garage.
With Leclerc and Vettel off track at Turn 7, the Ferrari benchmark remained, although Alonso could at least close to within 2.4s to move to third ahead of Daniel Ricciardo.
Stroll would pip Alonso before a string of mistakes at Turn 4 - Zhou, Pierre Gasly, Nicholas Latifi and Alex Albon combating understeer and oversteer to require the run-off on the outside of the medium-speed left-hander.
With conditions deteriorating, Lewis Hamilton and Leclerc vacated the cockpit completely to leave only Mick Schumacher out on track after 22 minutes.
Six minutes later, the track was comparatively busy as the standing water started to dissipate - this allowed the Haas cars climbed to 3-4 and the forecast showed no more rain would arrive as visibility improved.
That would not stop Gasly bringing out a yellow flag shortly after when he chopped the inside kerb at Turn 7 to spin, that preceded Russell continuing straight on at Turn 12.
This came as Mercedes struggled greatly to generate tyre temperatures at the rear axle most of all, something that prompted a shake of the head from Lewis Hamilton.
With Alonso returning to second, posting a 1m43.570s, as he persisted with the intermediates, Aston Martin driver Vettel then called out a red flag with nine minutes to run.
The AMR22 broke away from the retiring four-time world champion through the Turn 10 left-hander, initiating him into a spin to career across the gravel and biff side-on into the barrier.
The session would resume six minutes later, with Verstappen finally setting a representative lap as the chequered flag came out to move fastest, the RB18 clocking a 1m43.205s.
He was then immediately pipped over the line by Leclerc, the Ferrari driver - who moments before caught a 360-degree spin out of Turn 3 - improving to a 1m42.141s.
With Albon slotting in what would be third in the dying moment, then all eyes were on Latifi in the Williams.
He had held the fastest time of all through the first sector in the updated FW44.
And as the last driver to cross the line, the Canadian had stitched together a sequence of purple micro sectors to buzz over the line in 1m41.480s to find 0.6s over Leclerc.
This came despite having to go round an AlphaTauri at Turn 1 and plenty of corrections.
Verstappen, as a result, would be shuffled to fourth ahead of Russell and Alonso.
Meanwhile, FP1 topper Sainz would be relegated to seventh over Norris and Vettel’s final attempt.
Kevin Magnussen completed the top 10 over Hamilton, Schumacher and Esteban Ocon.
Ricciardo and Stroll led Zhou, while Tsunoda completed a messy session for AlphaTauri in 17th over Bottas, Gasly and Sergio Perez - the Red Bull completing the fewest laps with just 21 combined.
Full FP3 results:
| Cla | Driver | Chassis | Time | Gap | Interval | |
|---|---|---|---|---|---|---|
| 1 |  Nicholas Latifi |  | Williams | 1'41.480 | ||
| 2 |  Charles Leclerc |  | Ferrari | 1'42.141 | 0.661 | 0.661 |
| 3 |  Alex Albon |  | Williams | 1'42.381 | 0.901 | 0.240 |
| 4 |  Max Verstappen |  | Red Bull | 1'43.205 | 1.725 | 0.824 |
| 5 |  George Russell |  | Mercedes | 1'43.434 | 1.954 | 0.229 |
| 6 |  Fernando Alonso |  | Alpine | 1'43.570 | 2.090 | 0.136 |
| 7 | Carlos Sainz |  | Ferrari | 1'43.589 | 2.109 | 0.019 |
| 8 | Lando Norris |  | McLaren | 1'43.743 | 2.263 | 0.154 |
| 9 |  Sebastian Vettel |  | Aston Martin | 1'44.178 | 2.698 | 0.435 |
| 10 |  Kevin Magnussen |  | Haas | 1'44.655 | 3.175 | 0.477 |
| 11 | Lewis Hamilton |  | Mercedes | 1'44.832 | 3.352 | 0.177 |
| 12 | Mick Schumacher |  | Haas | 1'45.156 | 3.676 | 0.324 |
| 13 |  Esteban Ocon |  | Alpine | 1'45.570 | 4.090 | 0.414 |
| 14 |  Daniel Ricciardo |  | McLaren | 1'45.624 | 4.144 | 0.054 |
| 15 | Lance Stroll |  | Aston Martin | 1'45.638 | 4.158 | 0.014 |
| 16 |  Zhou Guanyu |  | Alfa Romeo | 1'45.691 | 4.211 | 0.053 |
| 17 |  Yuki Tsunoda |  | AlphaTauri | 1'45.850 | 4.370 | 0.159 |
| 18 |  Valtteri Bottas |  | Alfa Romeo | 1'45.930 | 4.450 | 0.080 |
| 19 | Pierre Gasly |  | AlphaTauri | 1'46.091 | 4.611 | 0.161 |
| 20 |  Sergio Perez |  | Red Bull | 1'48.240 | 6.760 | 2.149 |
| View full results | ||||||
