A silver medallist at last year's London Olympics, Fox again settled for second in the slalom canoe K1 event at Penrith Whitewater Stadium with Kudejova winning in 96.78 seconds.
The Sydney teenager was 0.7 seconds behind with Victorian Sarah Grant claiming the bronze in the first Australian senior selection race for 2013.
It was a sense of deja vu for Fox after earlier qualifying eighth fastest for the final from the semi-final, exactly the same turnaround from London.
"Obviously you want to win but Katerina Kudejova is one of the top girls in the sport and she raced better than me today and she did really well and I was happy with my race," she said.
"I will probably look back on it and think I can improve here and there but I think I was 0.7 behind, it is not too bad, I am happy."
An Australian also claimed silver in the men's C1 final with Perth paddler Robin Jeffery runner-up to German Franz Anton.
Anton weaved through the 18-gate course superbly to clock 91.47s, 2.22 seconds ahead of Jeffery, with Czech Republic star Stanislav Jezek third.
Jeffery was delighted with his performance.
"It feels fantastic," he said.
"I was hanging onto it a little bit in places and I was just really happy that I kept my mind on the next gate the whole way down so I was not dwelling on anything."