After finishing quickest in FP1 - and no driver who has done so this season has gone on to win a race - championship leader Verstappen shaved half a second off his time in that session to finish quickest in FP2.
Verstappen posted a time in his Red Bull of one minute 05.412secs to finish 0.336s ahead of surprise package Daniel Ricciardo in his McLaren.
Moments before Verstappen had clocked what proved to be the best time just after the half-hour mark of the hour-long session, Hamilton had set what would have been the fastest lap.
The seven-time F1 champion, however, had the lap deleted for exceeding track limits at the high-speed final turn 10, one of three overall in the session, leaving him down in fourth place behind Alpine's Esteban Ocon.
Bottas, meanwhile, was a lowly 12th, 0.839s adrift, but is under investigation by the FIA stewards for a spin as he pulled out of his pit box 15 minutes from the end.
After a set of hard tyres was fitted, Bottas sped away but lost the rear of his car, just avoiding the pit wall and coming to rest the other side of McLaren's pit crew.
While the McLaren team were kind enough to roll Bottas back into a position to get going, the team, however, made a complaint to FIA race director Michael Masi about the dangerous element of what had just unfolded.
The session had started with an 80 per cent chance of rain that never materialised other than a few drops in the opening minutes.
Nevertheless, it led to slightly tricky conditions, notably at the sharp turn three right-hander where Verstappen and Hamilton both ran wide on a couple of occasions on the hard tyres.
With dark clouds hovering, the switch to soft rubber arrived quicker than expected, with the lead changing hands numerous times as first Aston Martin's Sebastian Vettel, then Hamilton, then Ocon all went fastest.
Hamilton then did momentarily reclaim top spot by four-tenths of a second only for that time to be deleted, with Verstappen ultimately going top seconds later.
Alpine's Fernando Alonso finished fifth quickest ahead of Vettel and McLaren's Lando Norris, the latter duo just over half-a-second back.
Carlos Sainz, who suffered a spin early on, was down in 11th, with team-mate Charles Leclerc 13th, the Ferrari duo either side of Bottas.
Pierre Gasly, who had finished FP1 second quickest to Verstappen, sat out the entire session due to the discovery of a sensor issue with the AlphaTauri's Honda power unit.
GPFans is a multi-platform, multi-language brand dedicated to Formula One coverage. We bring you all the ins and outs of the sport, 24/7, everything from up-to-the-minute news and features to the latest viral stories and clips.
We believe that a new generation of exciting, outspoken drivers will make F1 more popular than ever before, and we want to give our users access to as much of their heroes as possible, on and off the track. From Lewis Hamilton to Max Verstappen, Daniel Ricciardo to Sebastian Vettel, we provide in-depth analysis of every every Grand Prix in the season, from Australia to Abu Dhabi.
With Formula One under the new ownership of Liberty Media, how the sport is being covered is evolving, and GPFans will look to be at the heart of this progression into new media, as one of the fastest-growing sites covering the king of motorsports.