Canadian Eliot Grondin made it back-to-back victories in Gudauri, and Bolton finished second in a close photo finish over Omar Visintin of Italy.
Bolton has won two medals this season and six career medals, while improving his World Ranking from fifth to third after five events this season.
"It was pretty crazy today, it was a little bit closer than yesterday", said Bolton.
"I tried to set Eliot (Grondin) up, he's riding so well, but there is a fair bit of draft and I tried to cross him in the finish on the right hand side and absorb, but sort of missed it and caught a bit of my tail on the lip and bounced."
"When I came out of the snow cloud I sort of thought maybe my tail was in the direct of the line, and saw Omar right there, so I thought maybe I just got it, but thought he probably had it, and on the transponders too is said he was a little ahead, but the transponder was on my front foot which wasn't near the line, so stocked to get it (second place) in a photo finish."
In the women's event, Brockhoff achieved her 17th career podium and third medal of the season.
Brockhoff moved through the quarter-final and semi-final rounds in second place to reach the big-final, where she led with French rider Chloe Trespeuch for most of the race, before Charlotte Bankes of Great Britain passed both athletes at the finish line to take the win, Trespeuch second and Brockhoff third.
NSWIS teammate Josie Baff also made it through to the small final, finishing sixth for the second time in Gudauri.
"I just wanted to have fun to be honest, I had about nine hours sleep over the past two days, so I was pretty tired and had a shocker of a race yesterday, so I just needed to figure out the start section and from there I just had fun," said the 31-year-old Brockhoff from Melbourne.
"It was really good racing the three other top girls and I knew it was going to be such a fight."
The result puts Brockhoff third on the World Cup standings, with Baff just behind in fifth place.
Also in action for Australia in the men's event was Adam Lambert in 32nd and Jarryd Hughes 44th.