On paper, this was the toughest assignment Wales will face in the group stage of World Cup qualifying given that the Czech Republic, in 31st, are ranked one place higher in the world than Wilkinson's team.
Montenegro, who Wales face in Llanelli on Saturday, are 84th in the Fifa rankings, while Albania are 71st.
Wales, like the Czechs, will be hopeful of beating Montenegro and Albania at home and away, meaning the matches between the two higher-ranked nations may well prove pivotal in deciding who tops the group.
With the return fixture to come in Cardiff in June, it is advantage Wales for now.
The visitors had wobbled in the early stages, with Olivia Clark saving from Aneta Polaskova before Bartonova pounced after Wilkinson's rearguard failed to deal with Michaela Khyrova's corner.
Rachel Rowe's excellent work then teed up Lily Woodham to cross for Cain to steer a first-time finish into the bottom corner.
Cain missed a golden chance for a second goal before half-time, the striker latching on to Ceri Holland's pass only to be denied by a diving Olivie Lukasova when through on the goalkeeper.
There was another set-piece scare for Wales when Klara Cahynova flashed a header wide before the hosts' second goal came from a half-cleared free-kick.
This time Bartonova turned provider, turning away from Hayley Ladd before chipping a cross which was turned in at the far post by Zufankova.
The Czech Republic thought the points were safe after Carrie Jones' shot was pawed to safety by Lukasova, only for Charlton striker Hughes to have the final say when her header crossed the line despite a touch from Lukasova.
Image source, FAW
