But in a bizarre finish, silver medallist Annemiek van Vleuten thought she had won the gold while Deignan also later admitted the chasing pack didn’t realise there was another rider up the road.
Kiesenhofer, who has a maths PhD from Cambridge University, attacked almost from the offset and was allowed to go well clear by the leading favourites, among them Deignan and a star-studded Dutch including the past two Olympic champions in Marianne Vos and Anne van der Breggen.
That leading group was whittled down to just three, including Israel’s Omer Shapira and Anna Plichta, of Poland, but the latter duo were caught just a few kilometres from the line.
After breaking clear to finish second, Dutch rider van Vleuten raised her arms aloft as though she had won the gold, unaware that Kiesenhofer had already crossed the line some way ahead of here.
From about 10kilometres out, it had become abundantly clear that the longtime leader was not going to get reeled in as the main group of favourites failed to put together a cohesive chase at Fuji International Speedway until late on.
For Deignan, it was another sour end to her Olympics. At London 2012, she was denied gold by Vos coming down The Mall, while her build-up to the 2016 race was overshadowed by controversy where she faced a potential ban for three whereabouts failures with anti-doping officials.
She was later cleared of any wrongdoing but went on to finish outside the medals, as she did again in Tokyo, a race that could yet prove her Olympic swansong.
For 30-year-old Kiesenhofer, who was never talked about as a potential favourite and does not even have a professional contract with a team in the sport, it proved comfortably the biggest win of her career.
Van Vleuten launched a late attack to take a silver she initially thought was gold with the bronze going to Elisa Longo Borghini.