Ceccon won with a time of 52.00 seconds, with China's Xu Jiayu 0.32sec behind for silver and Ryan Murphy of the USA in bronze.
The Italian, who was fourth in Tokyo, delivered Italy more joy following Nicolo Martinenghi's triumph in the 100m breaststroke on Sunday.
The 23-year-old Ceccon, who won the world championship in 100m in Budapest in 2022, picked up his second medal of the week after bronze in the 4x100m free relay.
"Ever since I was a kid I knew I could win this medal and today is that day," a delighted Ceccon told Italy's Rai television.
"I can't be happier. As a kid, at 15, the coach asked me: 'What is your dream?' I answered: 'To win the Olympics', and he said: 'Calm down'. It's always been my dream," he said.
"Winning here isn't like at the World Championships, it's a race that happens every four years. I went strong and tried to hold on until the end. And in the end I was exhausted," he added.
For China's Xu it was a frustrating silver medal, having also finished second in the same event in Rio in 2016.
Murphy, the 29-year-old from Chicago who won three golds in Rio in 2016 including in the 100m backstroke, was hoping to restore his dominance in the event but had to settle for bronze.
He also finished with bronze in the event in Tokyo and his latest medal was his seventh in total, spanning three Olympics.
"I feel good about it. That's a really talented field. What I've improved on over the years is being able to frame things really quickly," he said.
"Thomas and Xu, they're both really talented guys, they've been really good at this sport for a long time. They deal well with pressure. Being third behind them, I'm not disappointed," he added.
