The Victoria, B.C., native had just finished the 1.5-kilometre swim portion of the race in 15th position before suffering minor injuries after tumbling off his bike into a curb and metal guardrail.
Whitfield, who seemed to lose control over a speedbump, received stitches in his left foot, according to a team official.
The race was won by Alistair Brownlee of Great Britain in 1:46:25, while his brother Jonathan was 31 seconds off pace for bronze. Javier Gomez of Spain took silver with 1:46:36.
Kyle Jones of Oakville, Ont. was 25th with a 1:49:58 and Brent McMahon of Victoria, B.C. was 27th, finishing in 1:50:03.
Whitfield, who had previously won gold at the Sydney Games in 2000 and silver in Beijing in 2008, was Canada's flag bearer at the opening ceremonies.
Whitfield told CBC Sports Weekend host Scott Russell the crash came down to a matter of bad timing.
"I just hit the speedbump – there’s a speedbump on the course – we’d scouted it, I knew it was there, but I just hit it at exactly the wrong moment, just as I was switching my hands."
Despite his injuries, the triathlete seemed to be in good spirits.
"I just hit [the speedbump] on a funny angle and launched myself over my handlebars," he said. "I think I crowd surfed. What do they say? Let's leave that for concerts?"
As for those injuries, Whitfield said there were no broken bones but he’s nursing a sore collarbone and will be monitoring any possible fallout from striking his head.
"I have quite a few stitches in my big toe and I have quite a few solid gashes,” he said. “I now know where the artery in my foot goes, because it was bleeding pretty good.”
The 37-year-old survived a bike pileup to capture gold in Sydney, using a finishing kick to win the first-ever Olympic men’s triathlon gold medal.
"That is not how I pictured things," Whitfield said in a statement. "I hit the speed bump on a funny angle and I'm not sure what happened. I wanted to keep going but my bike was in pieces and my leg and foot was gashed up pretty good.
"There was no way. I was right there. I had one of the best swims I had in a while. We train four years for this and unfortunately it happens. I've had two incredible Olympics."