The 29-year-old tap dancer polled the most viewer votes to finish ahead of male rival Luke Jackson in the final of the BBC competition's second series.
He will now receive £50,000 in prize money and get to perform on the highly-rated US edition of the show.
After hearing the result, Flint dipped his head as the So You Think You Can Dance final 16 rushed to congratulate him.
"What a wonderful stage to do what I love and what I have a massive passion for," he beamed. "For everyone to vote for me and support me, it's been wonderful. I just feel amazing."
When asked by host Cat Deeley if he had a message for viewers, Flint added: "I was never in the bottom two because of everybody. It's been the best thing I've ever done in my life and my career."
Head judge Nigel Lythgoe said of Flint's victory: "It's gonna be a delight for me to take Matt to Hollywood. He's got great character, he's got great style, he's going to fit right in."
Flint and Jackson's fellow finalists Kirsty Swain and Katie Love were eliminated from the contest earlier in tonight's programme.
After their departure a tearful Swain stated that So You Think You Can Dance had "made [her] dreams come true", while a "lost for words" Love claimed to have "learnt so much" from the "amazing opportunity".
It was reported this week that So You Think You Can Dance will not return for a third series on the BBC.
> Click for our interview with Matt
> Click for our interview with Luke
> Click for our interview with Katie
> Click for our interview with Kirsty
Watch So You Think You Can Dance winner Matt Flint perform with finalist Katie Love below: