The Australian Institute of Sport (AIS) scholarship athlete was second fastest on both her runs in round six of the World Cup, held on the 2010 Olympic Winter Games track at Whistler.
Teammate, Emma-Lincoln Smith, had a difficult day, finishing in 17th place.
Chaffer was right on the pace from the outset, finishing second fastest on both runs and a total of only 0.17 seconds behind the winner.
Her second place moves her up to ninth in the overall World Cup standings, while Lincoln-Smith remains in seventh place.
“I was really happy with how I raced today, it was well beyond what I was hoping and expecting,” Chaffer said.
“Racing consistently has been something I've been working on this year and I’m happy I could do it today when it counted.
“I really enjoy this track, I like the atmosphere and how it flows, and today it all came together for me.
“I'd like to thank all the coaching staff and team for the help this week, as well as the AIS and OWI for their support of our program. And also to my support team and family for everything they do for me.”
The final round of the Skeleton World Cup will be held next weekend in Calgary, before the World Championships in Lake Placid, USA, a week later.