A day after Algeria's Imane Khelif clinched gold at 66kg, Lin sobbed on the podium having claimed the 57kg crown with a unanimous points decision win over Poland's Julia Szeremeta.
Lin bowed to all four sides of the arena, before kneeling down and banging the canvas with her fists.
During the medal ceremony, the 28-year-old was initially composed, before breaking down in tears as she stood atop the podium.
Lin said she had tried to block out all the "noise" over the past fortnight, during which she and Khelif had come under intense scrutiny.
"As an elite athlete it is important to shut myself off from social media and focus," she said.
"Some of the noise and news of course I heard through my coach, but I did not pay much attention."
Lin and Khelif have been the central figures in a furore that has drawn fire from the likes of Donald Trump and Harry Potter author J. K. Rowling.
Both boxers were disqualified from last year's world championships after failing gender eligibility testing, with Lin stripped of her bronze, only to be cleared to compete in the French capital.
On Saturday Lin, who like Khelif competed without controversy at the Tokyo Olympics three years ago, was cheered into the 15,000-seated Court Philippe-Chatrier at Roland Garros and again when her name was read out.
The Taiwanese hared into the ring and enjoyed a height advantage of 10 centimeters over Szeremeta, Lin using her superior reach and thrusting jab from the opening bell.
Lin momentarily had the more compact Pole backed onto the ropes with a flurry of punches with a minute left of the first round to go ahead on all five judges' scorecards.
The second round was more of a brawl but Lin kept her cool and her advantage, before sealing the deal in the third and final round, although the 20-year-old Pole refused to go quietly.
"I have had several years of struggle and heartbreak," said Lin.
"But my dreams have finally come true."
What's the controversy?
Lin and Khelif were thrown out of last year's world championships, which was run by the Russian-led International Boxing Association (IBA), but were cleared by the IOC to compete in Paris.
The International Olympic Committee (IOC) has overseen the sport at the Games because of concerns over the IBA's running of boxing, including questions over its finances, ethics and judging of bouts.
The IBA's president Umar Kremlev claimed at a chaotic press conference this week that Khelif and Lin had undergone "genetic testing that shows that these are men".
The IOC has leapt to the defense of both boxers, with president Thomas Bach saying they were born and raised as women, and have passports saying that. Neither is known to identify as transgender.
Both fighters have enjoyed strong support back home and been well-received by spectators in Paris.
Top Taiwanese sports officials have threatened legal action against the IBA.
Who is Lin Yu-ting?
Lin is a two-time world champion who grew up in Taipei in a troubled home.
She and her brother were fans of Japanese anime "The First Step", which features a bullied youngster who became a great boxer.
But it was seeing her mother's suffering at the hands of her father that led her to take up the sport in junior high school.
"I joined the boxing team hoping that I can protect my mother with my own strength," she once told Taiwanese television.
She was fast-tracked into the Taiwanese youth team and established herself internationally by winning a world title in 2018.
The Tokyo Games gave her a first taste of the Olympics, one that ended in disappointment when she lost in the first round.
A year later she bounced back to clinch a world championship gold again.