Junio, racing in his hometown, won both his races and clocked a cumulative time of 69.44 seconds.
Alex Boisvert-Lacroix, from Sherbrooke, Que., took second place in a total time of 69.68, while Edmonton's Jamie Gregg and Laurent Dubreuil of Levis, Que., were tied for third at 69.85.
"I'm really excited by it (placing first) and going to World Cups," said Junio. "It's a pretty good feeling. It's my first win in a long track competition. Both races went by pretty quick. I just thought about executing the points in my head. I had a checklist. Before I knew it (the race) was over."
Nesbitt, the London, Ont., native and reigning world champion in the 1,000 and 1,500 metres, won both 500-metre races in identical times of 38.246 for a cumulative of 76.48.
Danielle Wotherspoon, from Red Deer, Alta., was second in 77.07 ahead of Calgary's Anastasia Bucsis with a two-race total of 77.08.
The trials are used in identifying the teams for the first five World Cups of the 2012-13 season.
The first long-track World Cup will be held Nov. 16-18 in Heerenveen, Netherlands.