Jones, who hails from nearby Oakville, Ont., was one of three Canadian athletes in the men's 1.5 kilomtre swim, 40 km cycle, and 10 km run that took place Sunday morning at the Ontario Place West Channel.
After a strong swim, and a smooth transition onto the bike, Jones' race was unfortunately over before he could get to the halfway point of his ride.
"We were on the second lap in great position," he said recalling the incident. "One of the athletes went off the course on the other side of the cones, and when he tried to re-enter the course, he touched one of the cones and it shot right at my front wheel and punctured the tire immediately."
Jones attempted to make do with the damage, but was forced to call it a day.
"I kind of lost control of my bike a little bit, but I was able to stay up," he said. "The bike was pretty much unrideable."
For Jones, it was his first race of a major competition since having surgery on his leg last November.
"With family, friends, and everyone here today, I'm just really disappointed," said Jones. "The day was done earlier than expected.
"This is a race I've had on my radar for a long time."
Mexico's Crisanto Grajales took the gold medal with a time of one minute, 48:58s, while USA's Kevin McDowell (1:48:59) and Mexico's Irving Perez (1:49:05) finished with the silver and bronze, respectively.
While it was an unfortunate finish for the World Cup medallist and 2012 Olympian, his two fellow Canadians showed very well, with two top 10 finishes.
Caledon, Ont.,'s Andrew Yorke finished seventh with a time of 1:49:31, and was consistently with the lead pack during the bike race, and in second for the majority of the run.
Oak Bluff, Man., native Tyler Mislawchuk finished 10th with a time of 1:49:54.
Canada needed to have an athlete win the race in order to open the door for to compete in the Olympics next summer in Rio.