Northern Ireland's Craig Cathcart battles with Libor Kozak
NI U21s' hopes of European Championship qualification were ended as the Czechs grabbed victory at the Ballymena.
Two goals late in the first half put the Czechs in control with Zeman's free-kick followed by Kozac's header.
Oliver Norwood tested keeper Tomas Vaclik after the break but Dockal should then have made it 3-0.
Norwood's superb free-kick on 81 gave the Irish hope and they were denied a stonewall penalty late on when James McClean had his jersey pulled.
Josh McQuoid also missed an Irish chance right at the death.
Manchester United youngster Norwood emphasised his ability from dead-ball situations for the second successive European Championship qualifier as he curled in his free-kick from 25 yards.
It was a carbon copy of his superb free-kick against Germany, which had earned his side a draw.
However, on this occasion it could not prevent Steve Beaglehole's side slipping to their fourth defeat in five games in the campaign.
Irish keeper Trevor Carson denied the superb Zeman early on but the Northern Ireland custodian then misjudged a long ball and had to be rescued by Craig Cathcart who cleared Kozak's effort on the line.
Ryan McGivern whipped a dangerous ball into the Czech area in the 16th minute but Billy Kee failed to get the vital touch.
Zeman made the breakthrough in the 36th minute with a free-kick which flew through a sea of bodies and past Carson.
The Czechs struck again a minute later through a header from the towering Kozak after he had escaped marker Johnny Flynn.
Carson then did well to parry a close-range header from Michael Rabusic in the 50th minute but Vaclik then made a great save at the other end to tip a Norwood free-kick over the bar.
Dockal missed a sitter for the Czechs on 69 but Northern Ireland were back in with a chance nine minutes from time when Norwood curled in his glorious free-kick.
Vacha's jersey-pull on McClean should have resulted in a Northern Ireland penalty on 87 minutes and sub Josh McQuoid kneed a close-range effort into Vaclik's arms in injury-time.
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