The Mexican, who had been decidedly off the pace on Friday, returned to Spa and led the way over defending champion Max Verstappen, while Carlos Sainz headed up the Scuderia charge in third.
The Aston Martins were the first cars to hit the track, both drivers donning a set of mediums tyres to lead out Lewis Hamilton and Sergio Perez – the pair taking on the red-walled soft Pirellis.
Hamilton was the first to complete a lap but circulated seven seconds off the eventual pace to leave the Alfa Romeo double act as the first to post anything like a representative lap time.
After seven minutes of the hour, using a fresh set of C4 softs, Zhou Guanyu propelled himself to the top of the leaderboard courtesy of a 1m47.795s effort.
That placed him a little over a tenth quicker than his teammate Valtteri Bottas. The Finn was the fastest driver of all through sectors one and two but lost out in the final part of the lap.
Regardless, the Alfas were initially clear by 2.2s after 10 minutes – helped by Verstappen locking the front-right into La Source before complaining of all-round tyre overheating.
After 10 minutes, only the Ferrari and Haas cars had yet to emerge – the Scuderia likely working to save a set of tyres after an ill-fated strategy that bet on hards in Hungary.
With Hamilton struggling in ninth after a massive bout of oversteer through the Bus Stop chicane, before Daniel Ricciardo did similar, the Aston Martins charged to third and fourth, led by Lance Stroll.
Kevin Magnussen, Haas VF-22
Photo by: Andy Hone / Motorsport Images
Kevin Magnussen finally emerged after 21 minutes, the Dane suffering an electrical shutdown in FP1, but as he came out the other Haas was called back to the pits – the team having spotted an issue for Mick Schumacher after only six laps of running.
But Magnussen was straight into the groove, running third on a set of softs to lap just two tenths shy of Zhou thanks to the fastest run of anyone through S2 at that time.
It would be another four minutes before the Ferraris finally hit the track, with Sainz soon moving to the top of the charts thanks to his 1m46.461s qualifying simulation on softs.
Leclerc was four tenths slower than his team-mate after the first go, the Monegasque set for a hefty grid penalty for engine and gearbox changes along with Lando Norris, Schumacher, Zhou and Verstappen.
Red Bull responded as Perez turned in a 1m45.972s to run half a second quicker but Verstappen would remain only…