The 28-lap race was the second in a series organised to provide some entertainment for fans starved of real-life action due to the new coronavirus pandemic that has stalled most sport worldwide.
Sunday was originally scheduled to be the inaugural Vietnam Grand Prix but the virtual race, with the 20 drivers joining remotely from their homes, was staged on a version of Melbourne's Albert Park.
The Hanoi street circuit is not yet available on the official F1 video game.
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"It was unbelievably hard," said Leclerc, who led from start to finish and took the chequered flag 14.094 seconds clear of Danish Renault junior Christian Lundgaard with Williams F1 driver George Russell in third place.
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"We are sitting on a chair, so there is not even the G-force we have in a real car, but I am sweating like crazy," added the Monegasque, winner of two races last year in his first season with Ferrari.
"The muscles are not hurting but the concentration and everything, I've been sweating a lot."
Leclerc's 19-year-old brother Arthur was fourth for Ferrari, just ahead of Italian Alfa Romeo driver Antonio Giovinazzi.
Lundgaard would have started on pole but was given a five-place drop for exceeding track limits in qualifying.
Jenson Button, the retired 2009 world champion, was 11th with McLaren team mate Lando Norris failing to start due to technical problems for the second race running and Mexican Esteban Gutierrez also absent.
Norris's Twitch streaming platform still had more than 77,000 viewers at its peak while more than 190,000 watched Formula One's official livestream on YouTube.
Stokes finished last, behind retired grand prix winner Johnny Herbert, but the all-rounder acquitted himself well in a field with six current F1 drivers and gave a cheerful thumbs up from his living room.
China's Guanyu Zhou, winner of the first race for Renault on a virtual Bahrain layout, did not compete.
The next official virtual race is the Chinese Grand Prix on April 19.
Formula One is hoping to resume racing for real with a reduced 15-18 round calendar from the European summer, subject to the spread of the virus.
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