Dominique Maltais continues to lead the way in the World Cup standings having followed up Saturday's victory with a second place on Sunday.
The Canadian, a bronze medallist in the 2006 Turin games, was edged out of top spot by Samkova.
USA's Lindsey Jacobellis rounded off the top three and she remains a huge 840 points adrift of Maltais in the overall rankings.
"In the finals, I was leading the race almost all the way down but then I made a mistake. Eva was in great shape today and she deserves the victory," said Maltais, who has 3,400 points.
Great Britain's Zoe Gillings finished 20th – a result which does little to help her top-ten ambitions.
The 28-year-old, a veteran of two Winter Olympics, came into the event held in Andorra in tenth position overall in the standings on 790 points.
But she would have been hoping for better as the result leaves her now on 900 points, in 11th overall, having previously finished 17th on Saturday.
In the men's event, Italy’s Omar Visintin won and now leads the World Cup standings with 2,426 points.
Lucas Eguibar claimed the second spot while Luca Matteotti made his way onto the podium in third.