Hooker Ray Barkwill scored Canada's other try as they finished the qualification tournament with three wins and 14 points, ahead of Germany (nine points), Hong Kong (five) and Kenya (zero).
The North American side kept up their 100 percent appearance record at the global showpiece since it was first played in 1987 and will go into Pool B at the tournament with defending champions New Zealand, South Africa, Italy and Namibia.
"We’re over the moon, coming into the tournament we knew it was going to be tough, but with all the support from home and the work that has been put into this, it’s awesome," Canada captain Phil Mack said at the post-match presentation.
We came here with a goal in mind, but now the hard work really starts. We are going to enjoy this moment and then hit the afterburners and build to the World Cup.
After a tense first quarter in the wet of Marseille that was largely dominated by Hong Kong, Barkwill put Canada ahead as he powered over for the opening score, converted by flyhalf Gordon McRorie.
Canada's scrum half Phil Mack played his part in sealing a World Cup spot
Image credit: Getty Images
South African-born number 10 Matthew Rosslee landed a penalty for Hong Kong to reduce the deficit, but Canada held a 14-3 halftime lead when Van der Merwe crossed the tryline for his first score.
Winger Conor Hartley reduced the deficit to four points when he crossed for Hong Kong’s only try 13 minutes into the second half, but Canada pulled away in the final quarter to claim the win.
McRorie kicked two more penalties before Van der Merwe shrugged off a number of tackles to score his second try in the corner.
In the earlier game, Germany defeated Kenya 43-6 to complete a miserable tournament for the African side as they slipped to a third defeat.