The AIS Scholarship holder was one place higher than at last week's season opener in Whistler, finishing just over two seconds behind the winner, Germany's Anja Huber.
Lincoln-Smith's consistency highlighted the performance, with just 0.2 seconds separating her two runs down the 1988 Olympic course.
But the Narrabeen athlete had been hoping for a better outcome.
"I was frustrated with the result as I had been training well," Lincoln-Smith said.
"I knew I had it in me to get up there closer to the top girls, but I made a few mistakes on both runs in curve eight, which cost me a lot of time."
"I felt nice and calm on my sled, but was just not good enough today, which is hard to swallow."
"I'll just try and learn from it and move on and focus on next week's race in Park City."
Fellow Australian slider, Lucy Chaffer, was unable to repeat her 11th place from last week, and finished in 17th place.
After the opening two rounds in Canada, Lincoln-Smith is ranked 9th on the circuit with 296 points. Chaffer is 12th on 224 points. Today's winner, Huber, is the current World Cup leader on 425 points, 16 clear of her countrywoman, Marion Thees, with Canadian Melissa Hollingsworth third, a further seven points in arrears.
Round three of the Women's Skeleton World Cup will be held at the 2002 Olympic Winter Games course at Park City, USA, on Friday 10th of December.