Petr Jiracek scored the only goal of the game 18 minutes from time as the Czechs joined Greece - the 2004 champions - in the quarter-finals.
Few would have predicted such an outcome before the group games began and even fewer who saw the first halves here and in Warsaw.
Poland were totally dominant in the opening period but seemed to have left it all on the pitch in that first 45 minutes and they were second best after the restart.
But it was a mistake that cost them as Rafal Murawski tried to drive forward from midfield and lost the ball with little cover behind him.
It means Poland have never reached the knock-out stages of the Euros while the Czech Republic did so for the third time in five editions.
Given the hosts' absolute need to win it it was no surprise they set a manic tempo from the off and the first half hour must have made uncomfortable viewing for the visiting Czech fans.
Twice in the opening minutes the home fans let out a brief cheer but Dariusz Dudka's overhead bicycle kick and Ludovic Obraniak's free-kick both hit the side-netting rather than the back one.
The Czechs did have one sniff themselves but Vaclav Pilar swiped at thin air from 12 yards from Theodor Gebre Selassie's cross.
A horribly misplaced pass from Jaroslav Plasil was intercepted by Polish captain Jakub Blaszczykowski and he slipped in Borussia Dortmund team-mate Robert Lewandowski, but he sliced his shot well wide.
Such was Poland's dominance that even their defence started getting in on the act and Sebastian Boenisch shot wide when well placed before sending Czech goalkeeper Petr Cech scurrying across his goal to scramble the ball behind from a long-range volley.
Marcin Wasilewski threw himself at a cross from deep but his header was gathered easily by Cech.
Towards the end of the half Poland's electric pace - which seemed to have provoked a couple of flashes of lightning and an enormous crack of thunder - slowed markedly and the Czechs came back into it.
But a deflected Jiracek shot and Pilar's low effort did not overly tax goalkeeper Przemyslaw Tyton, who kept his place despite the return from suspension of Wojciech Szczesny.
The second half was the reverse of the first with Poland melting away and the Czech Republic piling forward.
David Limbersky skipped into the box but prodded wide before Tomas Sivok won a header from Plasil's free-kick inside the six yard box only for his downward effort to bounce up into Tyton's chest.
The big breakthrough came 18 minutes from time as Murawski surged forward from midfield but was dispossessed by Jiracek.
The Czechs countered three on three and Jiracek exchanged passes with Milan Baros before turning inside Wasilewski and slipping the ball under Tyton.
Wasilewski got up well to win a header in the box but it landed on the roof of the net as the hosts finally came alive.
With virtually the last kick of the match Michal Kadlec secured qualification for the Czechs as he headed Blaszczykowski's chip off the line.
Had that gone in, the Czechs would have been out.