Lithuania's Danas Rapsys beat the Olympic champion to the wall in a pulsating Gwangju final, only to be ejected for twitching on the starting blocks.
Briton Duncan Scott, who tied with Russian Martin Malyutin for the bronze, subsequently refused to shake Sun's hand on the podium - just as Australian Mack Horton did after losing to the Chinese giant in the weekend's 400m final.
Scott, the European champion, also declined to pose for an official photo, prompting Sun to bark angrily at him as they walked for their lap of honour.
Japan's Katsuhiro Matsumoto took the silver medal after the result shuffle.
Sun, now an 11-time world champion, is competing under a drugs cloud in South Korea after a leaked FINA doping panel report claimed he smashed vials of blood with a hammer after being visited by testers last September.
FINA cleared him to swim this week, but the World Anti-Doping Agency (WADA) appealed the decision to the Court of Arbitration for Sport, who will hold a hearing in September.