Just 0.072secs separated the Red Bull driver from F1 title rival Hamilton across the 7.004km of the Spa-Francorchamps circuit, with Mercedes team-mate Bottas sandwiched in between the pair.
But after his high-speed smash at Silverstone in the British Grand Prix, and opening-lap crash in the last race in Hungary, Verstappen planted his Red Bull into a barrier at the turn seven Malmedy right-hander late in the hour-long run.
Needing a clean weekend given the previous incidents, it was not what Verstappen would have wanted for his confidence in his ongoing battle with Hamilton in the F1 title race.
Verstappen simply lost the rear of his RB16B into Malmedy, leading to it hitting the barrier and breaking the suspension on the right-rear tyre, bringing out the red flags and ending FP2 as there were less than four minutes remaining.
As with the first practice session, F1 again struck lucky with the weather that allowed all the drivers two relatively dry hours despite the forecast for rain.
The starts to both sessions came after rain had fallen but with the circuit dry enough to ensure opening lap intermediate tyres were soon ditched for slicks.
Bottas emerged quickest from FP1 but on qualifying simulation runs in FP2, it was Verstappen who was fastest with a lap of one minute 44.472secs.
It is understood, however, the two leading teams ran with engine modes turned down in order to preserve life, with the possibility of 12 races to come over the second half of the season.
Mercedes is among those, though, running new power unit elements from this weekend, notably an internal combustion engine, turbocharger, MGU-H and MGU-K, providing its cars with an advantage for a high-power circuit.
At present, qualifying appears to be a straight fight between the leading trio, albeit Bottas will take a five-place grid penalty after instigating the lap-one crash at the last race in Hungary.
Behind Hamilton, Alpine's Fernando Alonso was the best of the rest, albeit a further four-tenths of a second adrift of the seven-time F1 champion, followed by Pierre Gasly in his AlphaTauri and Aston Martin's Lance Stroll.
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