A second half goal by Jitka Chlastakova in the 61st minute secured the win for East Europeans.
It was a physical first half which saw both teams going at each other in search of an early goal. The first chance fell to Czech Republic but Banyana Banyana captain Janine Van Wyk did well, throwing her body on the line to block an on-target Czech shot in the opening proceedings.
The South African women retaliated immediately, but Sanah Mollo’s long-range shot went over the Czech cross-bar a few minutes later.
The Czech Republic got another chance two minutes later, but South Africa’s goalkeeper Roxanne Barker managed to parry out the header for a corner.
Mollo was back in the thick of things 6th minute, but her shot in the box was no threat as it was comfortably dealt with by the Czech Republic keeper.
Barker did very well in the match as she took charge of her area, making a great save in the 13th minute from a free kick taken a couple of metres outside the box.
The South Africans kept their shape very well, not succumbing to the pressure by the Czech Republic, with Barker outstanding in goals keeping the score level at nil-nil going into the break.
USA-based striker, Jermaine Seoposengwe came on for Nompumelelo Nyandeni at the start of the second half. She made her presence felt immediately - hitting the cross-bar in the 54th minute with the opposition keeper well beaten.
Minutes later she came close to opening the scoring, but her long-range shot taken from a set-piece was easily handled by the Czech Republic keeper. Seoposenwe was a constant menace to the Czech Republic defence. In the 64th minute she won the ball from a goal-kick and out-ran a defender but her attempted shot went across the Czech goals.
Two minutes later it was the Czechs who broke the deadlock - beating Banyana Banyana’s off-side trap and Chlastakova managed to put one past Barker who had been exceptional throughout the match.
The goal seemed to spur Banyana Banyana on and they continued with their attacking play looking for an equaliser.
Mollo came close in the 80th minute, but her long-range shot was saved by the keeper, while Amanda Dlamini’s header in the box from a corner could not find the back of the net and the match ended 1-nil in favour of the Czech Republic.
Banyana Banyana finish in third place in Group C after Belgium and Mexico failed to find the net in the other Group C clash.
After three matches each, the South Americans end on top with seven points, the Czech Republic is second with four points, South Africa is a point adrift while Belgium managed just two points.
The Cyprus Women’s Cup comes to an end this week, with the positional matches scheduled for Wednesday, 11 March.
South Africa will now face Finland as they battle for 9th and 10th place in the tournament of 12 nations.
The match will take place in Nicosia and kick off is at 12h00.
The final will be contested by England and Canada; Italy and Mexico will fight for position three and four. The battle for 5th and 6th place will be between Australia and the Czech Republic with Scotland and the Netherlands vying out for 7th and 8th.
Republic of Korea and Belgium will face each other to see who finishes 11th or 12th.
The final will take place at 18h00 in Lanarca.