The 19-year-old cyclist, who won gold at the 2024 junior world championships in theindividual time trial, finished the 39.2km elite circuit around Montreal in 46 minutes and six seconds.
He was 73 seconds behind Belgium's Remco Evenepoel who secured the title for the fourth year on the trot. Filippo Ganna from Italy came second.
"I didn't want to take too many risks," said Seixas. "I feel in great shape and it's certainly a great source of pride to be up there with Evenepoel and Ganna on the podium."
Seixas, who came fourth last summer in his first Tour de France, is the first Frenchman to win a prize in the time trial since Jérôme Coppel took the bronze medal at the world championships in Richmond, Virginia, in the United States in 2015.
"I hope it will lead to more success in the race," added Seixas. "It's not just me. We've got a new generation coming through who'll be strong, and I hope that in future we'll be even better in the time trial.
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"In France, the discipline is developing quite well at the moment, and I'm pleased to have this medal to give the others confidence."
Seixas, who rides for the French stable Decathlon CMA CGM, said he plans to compete in the 273.7km road race on the final day of competition on Sunday.
"I hope my form will improve even further, even though it's already very good. A time trial isn't necessarily indicative of what will happen later in the week but I think I'm off to a good start.
"I hope to do better and finish on a different step of the podium."
Reusser retains women's title
Marlene Reusser retained the women's elite individual time trial with a winning time of 50 minutes, 24.44 seconds.
Britain's Zoe Backstedt claimed silver, finishing 40.11 seconds behind Reusser, while Germany's Franziska Koch took bronze, 45.54 seconds adrift of the 35-year-old Swiss.
The course wound through Montreal along the St. Lawrence River, over the Samuel De Champlain Bridge and through Circuit Gilles Villeneuve before tackling an uphill finish in Old Montreal.
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"On the one hand, I was looking forward to the course because it has so many challenges and technical aspects," said Reusser.
"But from the side of pacing, how fast you should go, to cope with the challenges, I was really nervous. We don't have time trials like this really."
On Monday, the men's and women's under-23 individual time trials take place around Montreal.
Seventy-two men from 47 countries will ride 32.3km around a circuit between Avenue du Parc and Parc Jeanne Mance.
The 52 female riders from 31 nations will cover 20.3km between the same points.
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