Euro 2012 qual. - Defensive Scotland suffer defeat
Scotland manager Craig Levein started with an ultra-defensive 4-2-2-2 formation with no recognised striker. Despite being hemmed in, Scotland survived until the 69th minute before Hubnik struck.
Tomas Rosicky's corner was flicked across the box by Roman Bednar and Hubnik pounced unmarked to nod the ball beyond visiting goalkeeper Allan McGregor for the winning goal.
Scotland led the section with Lithuania on four points before the night began and arrived in the Czech capital with the intention of snaring a point by opting for a formation they hadn't operated with before.
It soon became clear the night would not be easy on the eye.
Rangers forward Kenny Miller had scored 10 goals for his club in the Scottish Premier League, but was bizarrely left on the bench. He won his 50th cap after being thrown on alongside Burnley striker Chris Iwelumo in the final 14 minutes, but the damage had been done.
The visitors got away with their unappealing tactical ploy in a goalless first half, but only just as the home side dominated without converting.
With 10 men behind the ball, it needed the trickery of the home captain Tomas Rosicky to dance his way into the box on 19 minutes. He seemed likely to score, but flashed his shot wide of the target with his right foot from 12 yards out when a left foot finish may have brought greater rewards.
Lukas Magera then hesitated in the box when he thought he was offside, enabling the impressive Davie Weir to get back to clear.
When Scotland momentarily managed to break out of their own half, they almost went ahead. Marek Suchy swung a boot at Alan Hutton's cross, but the ball hammered off Chelsea keeper Petr Cech before flying to safety.
In a rare attacking moment, it perhaps illustrated the need for Scotland to be more positive. They never accepted the invite.
They visitors were soon back attending to defensive duties as Steven Whittaker nailed Tomas Hubschman. Rosicky swung in a terrific free-kick, but the ball broke off Hubnik before landing in the arms of a grateful McGregor on his line.
Scotland frantically scrambled the ball away when the willing Tomas Necid fired in a shot on 41 minutes before McGregor clawed Michel Kadlec's header over the bar from Rosicky's corner four minutes after half-time as the chances continued to pile up.
Scotland were restricted to feeding off scraps without any targets to knock the ball to in what was becoming an increasingly exhausting shift.
Rangers goalkeeper McGregor, one of the few highlights of a turgid and often demoralising night, was called into action to make a superb agile save on 67 minutes.
The dangerous Rosicky dinked a lovely ball to the back post. Jan Polak rose unmarked to head goalwards, but McGregor dived to claw the ball wide of the goal when it seemed destined to hit the back of the net.
He would soon be rendered helpless.
Scotland finally buckled in the final 20 minutes as Gary Caldwell was caught marking space when Bednar, on for Magera on 59 minutes, played provider for Hubnik to convert to the delight of the home fans.
Scotland remain on four points with Lithuania, but their large travelling support will view this as a chance lost in a five-team group where they are probably playing for second spot and a play-off place.
Levein will have to rethink his strategy for Tuesday night when world champions Spain are the visitors to Hampden Park, but he is likely to bin a unique 4-2-2-2 formation that must be branded a complete failure after such an exacting and pointless evening.
The Czech Republic are ranked at 37th in the FIFA rankings, but Scotland paid the price for giving them too much respect.
They may well live to regret being so negative when the section concludes next year.