After setting the fastest time on the first of three runs, the West Australian was fifth on run two, and then slid back to sixth place at the finish, just 0.6 of a second behind overall winner, Sarah Reid, from Canada.
The first of nine World Cup meets was held on the 1.455 kilometre course at Lake Placid, with 20 curves and an average gradient of 6.8 per cent testing the world's best sliders. Maximum speeds were around 120 km/h, and Chaffer was happy with her season start.
"It feels good to get the season going," Chaffer said.
"I was happy overall with my runs, but a few mistakes meant I dropped a few spots. However, I'm happy with starting the season with a top six."
After a 12-month break from the sport, fellow AIS slider, Michelle Steele, was impressive and finished in 12th place. She missed the final heat for the 10 fastest competitors, but took plenty of positives from her performance.
"I was pleased to be back on the ice and racing in the World Cup after 12 months off," Steele said.
"I am happy with two solid runs and a 12th place finish in my first race back."
In addition to the World Cup meet, Australians Melissa Hoar and Emma Lincoln-Smith competed in the North American Cup event, finishing in second and fifth place respectively.
"Each of the girls has developed a great level of comfort on their sleds and are confident of a strong showing this season," OWIA Program Manager, Dale Chapman, said.
"This season is a really important part of the puzzle for our Olympic aspirations. The major outcome we are seeking from this season is to finish as a nation ranked in the top four, which will give the team three positions on the World Cup tour in the Olympic season.
"This will then give us the maximum chance of qualifying three athletes through to the Olympics in Sochi, Russia, in 2014."
The next round of the FIBT Skeleton World Cup is in Park City, USA, next weekend.
In the Women's Bobsleigh, Australian pair, Astrid Radjenovic and Fiona Harrison, finished 15th.