Owens and Kneller, both Australian Institute of Sport and New South Wales Institute of Sport scholarship holders, finished in 15th and 20th places respectively.
The women's event was won by Sweden's Anna Holmlund, with Swiss skier Katrin Mueller second and France's Ophelie David in third place, while Finn Jouni Pellinen was victorious in the men's final ahead of Austrian Andreas Matt and Germany's Daniel Bohnacker.
Matt's second place means that he has won this season's ski cross World Cup, now that he holds an unassailable lead of 244 points over Canada's Christopher Delbosco.
Last night's results leave the Australian women's and men's number ones in a battle for a place in the top 10 World Cup rankings.
Owens, who is currently in ninth place on the standings, having slipped one position after her performance in Meiringen-Hasliberg, appears to have secured a year end top 10 ranking with two rounds remaining before the close of the season.
However, Owens still needs to ski well in the two remaining races in Sweden and Norway to hold out Austria's Andrea Limbacher, who is currently in 10th spot, 23 points behind the Australian, and Czech skier Nikol Kucerova, just a another 12 points back.
Both Owens' top 10 rivals finished higher than the Australian in last night's results, making her task a little less cut-and-dry.
Kneller also dropped a place, going from 12th to 13th and is 24 points behind the current 10th ranked skier, Switzerland's Alex Fiva.
Both Australians finished third in their knock out finals, which is based on a system that allows only two of the four skiers from each race to advance to the next round.
Teammates Katya Crema and Sami Kennedy narrowly missed the 16-place women's finals, qualifying in 17th and 19th place, just outside the cut-off.
The team now heads to Branas in Sweden for the season's penultimate round on March 13.