Yurkiw, from Owen Sound, Ont., took the title with a time of one minute 4.25 seconds on a fast track at the Dave Murray National Training Centre.
Gagnon, from Lac-Etchemin, Que., was second in 1:04.63.
Yurkiw won her first national title since 2008, when she claimed both the downhill and super-G crowns.
"I'm happy to have it back. It's been a long time and I skied really well today," Yurkiw said. "I risked in the right places and I feel good.
"I just stuck to my plan and tried not to change too much. Sometimes when you are on a track for a few days you start overthinking things and (going into) too much detail can be too much. I try to just keep things simple and I think I did my job."
Julia Roth of Waterloo, Ont., was third in 1:05.34. Valerie Grenier of Mont-Tremblant, Que., and Sarah Freeman, of Pincher Creek, Alta., tied for fourth in 1:06.02.
Gagnon is better known as a giant slalom and slalom skier, but made strides in downhill at the World Cup level this season.
"Today (Larisa) got me by a little more than I wanted but I'm really happy because she's a great downhiller and I'm happy that I've been competing with her all week," Gagnon said.
"I like this track. It got faster every day, which makes it more fun. The jumps are getting bigger and bigger and the speeds are high. I’m having a lot of fun. I'm hoping to sweep as many gold (medals) as I can here — we'll see what happens."
Competition continues Monday with the men's and women's super-G.