The 24-year-old Bencic edged out Vondrousova 7-5, 2-6, 6-3 on her second match point, with the final finishing at 11:28 pm local time (1428 GMT) after two-and-a-half hours on court.
Bencic will also play in Sunday’s women’s doubles final alongside Viktorija Golubic against Czechs Barbora Krejcikova and Katerina Siniakova.
The moment is yours, @BelindaBencic🥇🇨🇭#Tokyo2020 https://t.co/dN2jNw4sGr
— wta (@WTA) 1627743391000
She is looking to become the fourth player to win singles and doubles golds at a single Olympics, after Serena and Venus Williams and Chilean Nicolas Massu.
The ninth seed is the first Swiss to take singles gold since Marc Rosset at the 1992 Barcelona Games.
It is the biggest victory of Bencic’s topsy-turvy career.
Bencic appeared to have a big future ahead of her when she reached the US Open quarter-finals as a 17-year-old in 2014. But she struggled with injuries and slipped out of the top 300 in 2017.
She fought back impressively and reached a career-high ranking of fourth last year shortly before the Covid-19 pandemic hit, but has failed to win a WTA title since.
It was a disappointing loss, though, for the 22-year-old Vondrousova, who was also beaten in the 2019 French Open final, after belying her ranking of 42 with wins over Naomi Osaka and Elina Svitolina en route to the gold-medal match.
She fell just short of becoming the Czech Republic’s first Olympic tennis champion.
Bencic forged ahead by claiming the fifth break of a 59-minute opening set in the 12th game.
But her game deserted her in the second set as Vondrousova upped her level, breaking in a long opening game before cruising through it to force a decider.
Both players struggled on serve again at the start of the third as the tension took its toll, with the pair sharing four breaks in the opening six games.
Bencic had a medical timeout for treatment for what appeared to be blisters on her right foot after holding for a 4-3 lead.
That did the trick as she then broke to love to move to the brink of victory and she managed to serve it out, saving three break points and clinching the gold medal when Vondrousova sent a backhand return long.