Sionko almost had a second goal in the 29th minute when goalkeeper Ricardo flapped at another corner, but Joao Moutinho cleared his header off the line.
The Czechs battled bravely for an equalizer, but Sionko saw his 83rd-minute header tipped over by Ricardo from yet another set-piece when it seemed he should have scored.
With his side showing no sign of a breakthrough, Le Guen resorted to a double substitution, with Kris Boyd and Chris Burke replacing Dado Prso and Libor Sionko.