Discus thrower Aled Davies was overwhelmed with emotion at the ceremony as Kate hung the gold around his neck to the cheers of an 80,000-strong crowd in the stadium.
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Afterwards, the 21-year-old athlete – who was born with a condition that means he has limited movement and no muscle growth in his right leg – described having her presiding as "an honour".
"Such as a lovely person. Crazy to think I am a Paralympic champion," he tweeted.
The Duchess had been invited to present two medals and her spokesman said it was a "happy coincidence" that the first recipient was British.
After his win, Aled draped himself in a Union Jack and declared himself "the happiest man on the planet".
The discus thrower's triumph marked a glittering weekend for Britain, with athletes adding seven more golds to take their tally to 52 medals in total.
And Britain's athletes overtook their 2008 track and field total after just two and a half days of competition.
There were also gold medals for Anthony Kappes in cycling, Jessica-Jane Applegate in swimming, Sophie Christiansen in the dressage and for the mixed coxed four in rowing.
Kate was joined by the Earl and Countess of Wessex and their daughter Lady Louise in cheering on the rowers' win at Eton Dorney