The Czechs, remain two points behind Iceland in Group A after dominating much of the possession but had trouble breaking down a determined Kazak defence.
Yuri Logvinenko put the visitors ahead in the 21st minute when he out-jumped his marker and gave a sprawling Petr Cech no chance.
The home side levelled in the 72nd minute when Borek Dockal lofted a cross that substitute Skoda headed home for his first international goal.
Skoda added his second in the 86th minute when he rose to head a Josef Sural cross into the net.
(Reporting by Michael Kahn; Editing by)
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