The Canadian, who is fighting for a new contract to stay on the grid with the Grove team, surprisingly surged to the top in the closing moments of a slippery FP3 to outpace second practice Leclerc.
Alex Albon, who had taken the flag moments before his Williams team-mate, secured third ahead of his former Red Bull teammate and defending champion Max Verstappen.
A downpour in the hour leading up to FP3, which helped flood the paddock and caused some motorhomes to leak, made for a cautious start to Saturday’s one-hour session.
Leclerc was the first car out after three minutes, closely followed by teammate Sainz and then both McLarens, Zhou Guanyu’s Alfa Romeo, Lance Stroll and Mick Schumacher joined in the action .
The full wet tire was the pick of the pack, Leclerc taking the blue wall rubber to an initial 1m46.044 before Sainz found half a second to provisionally lead the pack.
Two-time champion Alonso then ventured into intermediates, requiring many corrections over the course of the lap and was eventually 5.8 seconds off the pace as the crossing point was still to come.
Charles Leclerc, Ferrari F1-75
Photo by: Glenn Dunbar / Motorsport Images
The full wets continued to be the optimum tire for the conditions as Leclerc needed just 10 minutes to record his 1m43.364s effort which would see him lead the standings for most of the session.
This gave him a 1.25s cushion over Sainz before heavier rain arrived, with neither Red Bull nor Mercedes car having come out of the garage.
With Leclerc and Vettel off the track at Turn 7, Ferrari’s benchmark stood, although Alonso was able to at least close to 2.4 seconds to move into third ahead of Daniel Ricciardo.
Passeig would pass Alonso before a series of mistakes at Turn 4: Zhou, Pierre Gasly, Nicholas Latifi and Alex Albon battle understeer and oversteer to require the run on the outside of the medium-speed left-hander .
With conditions deteriorating, Lewis Hamilton and Leclerc left the cockpit entirely to leave only Mick Schumacher off the track after 22 minutes.
Six minutes later, the track was relatively busy as the standing water began to dissipate; this allowed the Haas cars to go 3-4 and the forecast indicated that no more rain would come as visibility improved.
That wouldn’t stop Gasly from bringing out a yellow flag soon after when he clipped the inside curb at Turn 7 to spin, which preceded Russell continuing down the Turn 12 straight.
Alex Albon, Williams FW44
Photo by: Zak Mauger / Motorsport Images
This came as Mercedes struggled mightily to generate tire temperatures on the rear axle in particular, prompting Lewis Hamilton to shake his head.
With Alonso returning to second place, clocking 1m43.570, 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 four-time world champion as he retired through the left-hand Turn 10, setting him on a run through the gravel and a sideways hit into the barrier.
The session would resume six minutes later, with Verstappen finally setting a representative lap as the checkered flag went out fastest, the RB18 clocking 1m43.205s.
He was then immediately overtaken over the line by Leclerc, the Ferrari driver – who moments earlier took a 360-degree spin out of Turn 3 – improving to 1m42.141s.
With Albon moving into what would be third at the death, all eyes were then on Latifi in the Williams.
He had set the fastest time of all during the first sector in the updated FW44.
And as the last driver to cross the line, the Canadian had stitched a sequence of purple microsectors to cross the line in 1m41.480s to find 0.6s over Leclerc.
This was despite having to spin an AlphaTauri at turn 1 and many corrections.
Verstappen would, as a result, finish fourth ahead of Russell and Alonso.
Meanwhile, Sainz, leader of FP1, would be relegated to seventh place in front of Norris and Vettel’s last attempt.
Kevin Magnussen completed the top 10 ahead of 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 – Red Bull completed the fewest laps with just 21 combined.