Two goals in the space of eight first-half minutes, the first setting the tone for Matt Elliott's miserable evening by going in off the Leicester defender, gave the Euro 96 finalists a grip on the game they seldom looked like relinquishing.
Gary McAllister, returning as captain for his 57th cap after the injury which kept him out of last year's World Cup finals, bore the brunt of the home crowd's frustration. Shamefully booed after a mistake which almost allowed the Czechs to go 3-0 up, he was spared further punishment when Craig Brown replaced him with Don Hutchison.
Ironically, Scotland halved the arrears almost immediately through Eoin Jess, and twice came close to an equaliser. But the Czechs held out for a victory which takes them eight points clear of the Scots, who must now secure an unlikely victory in Prague on 9 June to have any hope of winning Group Nine.
Brown remained defiant afterwards that such a result was not beyond Scotland. "I would say to the Czechs that we feel we can go there, having had a good rehearsal in our friendly in Germany (on 28 April), and come back into contention for the automatic qualifying place," the Scotland manager said.
"We were written off in our last World Cup campaign after we drew with Estonia in Monaco, yet we went on to win the next five matches. We feel it's possible that we could win our last six this time. The reaction of the Czech team at the end was a compliment to us - anyone would have thought they'd won Euro 2000 itself."
Brown was also quick to defend McAllister, describing the booing as "disappointing" and likening it to the heckling of Brian McClair by elements of the Scottish support during Andy Roxburgh's reign. "I hope it was a small minority because Gary is a very popular figure in the dressing-room. He has just come back from a horrendous injury and he deserves encouragement."
McAllister would have been the first to admit that it was not among his better performances, although typically he continued to demand the ball when lesser players would have hidden. Brown insisted that his replacement had been purely for tactical reasons, though his decision was surely informed by a sense of compassion towards a player who has served Scotland well over the past decade.
Sadly, the Coventry playmaker was not alone in enduring an off-night. Elliott, in particular, looked ill at ease and prone to surrender possession as the Czechs sought to hit Scotland with quickfire counter-attacks.
The most conspicuous successs for Scotland was, curiously, a player starting an international for the first time. Neil McCann, pressed into service as a striker, drifted in his natural role on the left wing to dangerous effect during a strong Scottish opening, but there was no Joe Jordan or even a Duncan Ferguson to get on the end of his crosses.
Jess narrowly failed to meet one McCann centre, while the latter forced an athletic tip-over from Pavel Srnicek following one of numerous long throws by David Hopkin. Srnicek also beat aside a Hopkin header and was relieved to see Jess prod wide from a McAllister corner.
Yet Neil Sullivan had not made a significant save before the Czechs went ahead after 27 minutes, when Pavel Nedved's inswinging free-kick flew in off the side of Elliott's head. Before the Scots could retaliate meaningfully, Patrik Berger created the second for Vladimir Smicer, who exploited David Weir's lack of concentration to curl his shot round Sullivan and in off the far post.
The 6ft 6in Vratislav Lukvenc squandered the best of several Czech chances on the break. When Jess headed in his second goal for his country midway through the second half, following another prodigious Hopkin throw, Scotland came to life. Even in stoppage time, Weir and Hutchison might have scored, but their best chance of qualification now appears to be a play-off.
SCOTLAND (3-5-2): Sullivan (Wimbledon); Weir (Everton), Elliott (Leicester City), Boyd (Celtic); Hopkin (Leeds United), Burley, Lambert (both Celtic), McAllister (Coventry), Davidson (Blackburn); Jess (Aberdeen), McCann (Rangers). Substitutes: Johnston (Sunderland) for Davidson, 52; Hutchison (Everton) for McAllister, 64.
CZECH REPUBLIC (3-6-1): Srnicek (Sheffield Wednesday); Hornak, Votava (both Sparta Prague), Suchoparek (Strasbourg); Poborsky (Benfica), Nedved (Lazio), Berger (Liverpool), Hasek (Sparta Prague), Smicer (Lens), Nemec (Schalke 04); Lokvenc (Sparta Prague). Substitutes: Cuka (Nuremberg) for Lokvenc, 70; Rada (Slavia Prague) for Poborsky, 75; Baranek (Sparta Prague) for Smicer, 84.
Referee: K M Neilsen (Denmark).
n Sergei Terekhov scored twice as Estonia won 2-1 in Lithuania in yesterday's other Group Nine match. The result puts Estonia level with the Scots on seven points after five matches.
Wales run out of steam;
Round-up, page 29