The native of Sainte-Julie, Que., posted a time of one minute 25.189 second to finish behind South Korea's Park Se Yeong (1:25.155). China's Shi Jingnan was third in 1:25.225.
Hamelin was also fourth in the men's 3,000-metre race but wasn't entirely happy with having to settle for silver in the 1,000.
"I'm a little disappointed with only getting the silver," said Hamelin. "I was on my way to a gold medal when the two Koreans teamed up, sacrificing one so the other could win.
"One pushed me in the last turn (Sin Da Woon, who was penalized) and I ended up second. It's the only distance where I haven't won the world title yet and I would have liked to do it today. I have three years to make it up. Still, I'm pretty satisfied with how I've done at these world championships."
Hamelin collected Canada's only two medals in individuel races over the weekend, claiming a bronze medal over 1,500 metres Saturday. He finished fourth in the overall World Cup standings.
Rookie Kim Boutin of Sherbrooke, Que., was sixth in the women's 3,000-metre final and finished seventh in the overall standings.
"I didn't expect to make it to the 3000-metre superfinal, so it's really a pleasant surprise," said Boutin. "I'm quite happy with my first year at the senior international level.
"It makes me even hungrier for what's coming up in the near future."