A Kalas goal was enough for the Czechs to beat the Super Eagles in Austria.
Super Eagles boss Gernot Rohr started off with a three-man defence with John Ogu playing from the left side to support the 'Oyibo Wall' pairing of William Troost-Ekong and Leon Balogun.
Wilfred Ndidi was back and joined Mikel John Obi and Alex Iwobi in midfield while Victor Moses supported Odion Ighalo in attack.
The Super Eagles had a slow start again, allowing the Czechs to move the ball around.
But it was the Super Eagles who had the first shot on goal in the 5th minute, Moses testing the goalkeeper from a freekick after Mikel had been fouled.
The game settled as both teams tried to break each other before the 12th minute when Moses broke on a counter, but his effort after beating his man to drive into the box was blocked.
Three minutes later, Moses wasted a freekick after Ighalo had been fouled before the Czechs turned on the pressure.
Super Eagles goalkeeper Francis Uzoho saved a shot from inside the area after the Czechs threatened from a corner and six minutes later, the Europeans scored.
Uzoho's reflexes were sharp to save a header from a corner but Tomáš Kalas pounced on the rebound to put the Czechs ahead.
The Czechs were still on and broke on a counter in the 29th minute, Patrick Schick beat Ogu but shot wide after beating Balogun for pace.
A minute later, Moses found Ighalo in the box but the striker's left-footed shot was straight at Czech goalkeeper Tomáš Vaclík.
Ndidi's long-distance shot was saved by Vaclík in the 35th minute while the Czech goalkeeper was positioned well to save an acrobatic effort from Ighalo.
Like they did against England, the Super Eagles kicked off the second half on the front feet with Iwobi in the heart of it. The Super Eagles were on now and Moses did well to find Ighalo but his shot from outside the area was too weak to trouble the goalkeeper.
In the 59th minute, Brian Idowu shot wide after good work by the Super Eagles before the game was stopped because of rain.
five minutes later, play resumed and the Super Eagles continued from where they stopped.
The Super Eagles were moving the ball around and creating some chances. In the 67th minute, a Moses' cross was headed straight to the goalkeeper while Idowu could not keep his effort down after picking up the ball in the box with only Vaclík to beat.
Rohr introduced some new players, bringing in the Simy Nwankwo and Elderson Echiejile for Ighalo and Idowu respectively.
With a 1-0 lead, the Czechs sat back, looking to hit the Super Eagles on a counter and they did in the 77th minutes, but Uzoho was on hand to save a strike from outside his area.
The Nigerian goalkeeper also went down well in the 78th minute to save a header with his leg.