Flynn's accurate, front-foot style enabled him to keep the rangier Fitzpatrick at bay and claim Scotland's first gold medal of the Games.
The 20-year-old had caused something an upset by coming from behind to outpoint Welshman Joe Cordina in the Friday semi-finals.
And despite sustaining a cut over his right eye early in the fight, Flynn boxed with maturity to control the fight throughout and thoroughly deserve his unanimous points win.
Flynn, who jumped onto a corner post in celebration at the final bell, looked overwhelmed when the decision was announced.
Josh Taylor survived a torrid final round to win a second gold medal for the host nation in the men's light-welterweight category.
Taylor's clever, back-foot boxing helped keep Namibia's Junias Jonas at bay for the first half of the contest but his opponent was to prove no pushover.
Taylor's cleaner work proved decisive but Jonas still succeeded in drawing the Scotsman into a fight and doggedly pursued him round the ring in the final round.
But there was no doubt Taylor deserved to win all three rounds on all the judges' cards, bringing the first finals session to an end in style.
Flynn said he realised he had to turn the contest into a "war" to come out triumphant.
The 20-year-old said: "I knew he was going to come out firing and straight away he runs out - bang, bang, bang. I knew I had to step to the side and go to war with him. And it worked.
"All the tippy-tappy stuff was out the window. I knew I needed a high work-rate but it's hard when he's so awkward."
The Motherwell boxer said he was "buzzing like a jar of wasps" after the victory and the experience of fighting in front of a home crowd of almost 13,000.
"The roar was unbelievable," he said. "It was silence, bang, the shot lands and you just hear it echoing up and up and up. It was like a thunderstorm, a volcano.
"You feel it in your chest when you're in there, roaring in your chest."
He was inundated with well-wishers as he made his way from the ring but he could not make out any of his family.
"They were like ants," he said. "An army of ants that sound like an army of lions."
Taylor was overcome with emotion as Flower of Scotland rang round The Hydro for the second time in quick succession.
"I almost couldn't sing it, I couldn't hold my emotions together," said Taylor, who won silver in 2010. "Tears of joy, not tears of disappointment this time, thank God.
"I imagined it being amazing and everybody singing, but that was just surreal. It was a thousand times better.
"I could only sing it in bits because I would have broken down in tears. My body feels numb right now, I can't believe it."
The Prestonpans fighter was confident he had taken the first two rounds and recovered after taking a big shot in the final round.
"I knew he was going to come out at me in a big last round and I just wanted to make sure I got home safe and make sure I got that gold medal," Taylor said. "I didn't want to walk into any silly shots.
"I think I've boxed as well I've ever boxed in this tournament, I've had some world-class performances."