Fernando Santos' men now have an uphill task to qualify for the next stage of the tournament as they fell victims to two defensive mistakes in the early minutes of the game
Michal Bilek's men hit the Galanolefki with a first-half double salvo courtesy of goals by Petr Jiracek and Vaclav Pilar, and it looked like the Narodak had done enough to emerge winners.
After the break, however, a howler by Petr Cech allowed Theofanis Gekas to claw one back, but it was too little too late as the Czech claimed an important victory in their quest for a place in the quarter-finals of Euro 2012.
The game got off to the worst possible start for Greece as by the sixth minute it was trailing by no less than two goals. The makeshift defensive pairing of Kyriakos Papadopoulos and Kostas Katsouranis was struggling right from the off, and the Czech Republic wasted no time in punishing the Ethniki.
First, Tomas Hubschman exploited the space between the two central defenders to pick out Jiracek just outside the box, and the Wolfsburg midfielder slotted home easily under little pressure from the Greek rear guard.
Then, three minutes later, Theodor Gebre Selassie showed Jose Holebas a clean set of heels on the right wing before whipping in a cross, which was rather fortunately met by the feet of Pilar, who netted his second goal in as many matches.
Greece managed to shake off the early shock, but was soon dealt yet another blow as goalkeeper Kostas Chalkias picked up an injury and had to be substituted by Michalis Sifakis. Still, with the Czech Republic taking its foot off the gas, Fernando Santos' men began to gather momentum.
In the 40th minute, Greece had the ball in the net as Giogos Fotakis finished past Cech with a skillful header, following a cross from the right flank by Vassilis Torossidis, but the assistant referee had his flag up, meaning the goal did not stand.
The flow of play hardly changed after the break as the Czech Republic were dominating the proceedings, allowing Greece chances only on the break. Out of nowhere, however, the Ethniki managed to score after a horrible error by Cech.
A stray cross by Georgios Samaras in the box was inexplicably dropped by the goalkeeper in the path of Gekas, who had no trouble converting with the open goal at his mercy, halving Greece's deficit and giving them a way back in the game.
The goal gave Fernando Santos' men a much needed momentum and the Czech Republic soon found itself pinned back in its own half. Greece bombarded the penalty area with crosses, but Michal Bilek's players were doing their best to hold on to their lead.
The Ethniki threw everything forward in the final minutes of the game, but were ultimately denied an equalizer by the resilient Czech Republic, which claimed a crucial victory in its battle for a place in the quarterfinals of Euro 2012.