He qualified in eighth in the 63-boat field with a faultless 100.78sec run on the technically challenging Tacen course and dropped a spot in the final, after touching the sixth gate and earning a two-second penalty.
German Fabian Doefler won by just 0.2 seconds, heading off Italian Andrea Romeo with a winning time of 97.12.
Jones stumbled in her final, with a faint touch on gate 14 throwing off her rhythm. She missed two of the next three gates and eventually finished in 10th in a strong field headed by Slovakian Jana Dukatova.
But her progress past the semifinal stage marked a major milestone, a week after finishing 12th at the first world cup of the year in London.
"Obviously the final didn't go to plan but I had a clear semifinal and it's definitely satisfying to be building some consistency at this level," Jones said.
The Kiwi pair now move on to familiar water in the Czech Republic, where both have been based in Prague during recent seasons, for next week's third world cup.