Bottas is now effectively on provisional pole position for the race, with the FIA having confirmed that the starting grid will be formed from the FP2 result if Sunday's rearranged qualifying cannot be held.
Saturday's action has been cancelled amid safety concerns as Typhoon Hagibis approaches Japan.
Max Verstappen impressively split the Mercedes and the Ferrari cars, with CHarles Leclerc and Sebastian Vettel unable to improve their lap times sufficiently when attempting quick laps right at the end of the session.
Although track conditions ought to have played into their favour, the mass of traffic on the circuit, as others finished off long-runs, hampered them.
Carlos Sainz secured a pair of seventh-place spots, and a further boost for McLaren came with rivals Renault languishing way down the timesheets, having brought a new front wing to Suzuka.
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.