Even for Scotland, a nation that has an unparalleled record of international heartbreak, this was sore. Scotland suffered as cruel a denouement to an engaging 93 minutes as even their most seasoned of followers could have witnessed before.

One errant blow of a referee's whistle inflicted a hammer – and probably fatal – blow on the Scots' aspirations of a first appearance at an international tournament since 1998. The basic detail shows that Michal Kadlec's penalty ensured a share of four goals, but Scottish fans, players and management were consumed by a sense of injustice long before the ball hit the back of Allan McGregor's net.

Jan Rezek was the target for Scottish anger after the Czech Republic substitute threw himself to the ground when challenged by Danny Wilson. There is no question that Rezek dived, with the referee Kevin Blom sufficiently duped by the player's actions to award a penalty.

Plenty of pious nonsense is routinely spoken about play-acting from foreign players – those in the United Kingdom are perfectly capable of the same behaviour – but Rezek's actions are worthy of condemnation. Blom, suffice to say, may have to wait a while before being handed another crucial international encounter.

Amid frantic scenes, Scotland had time to claim a penalty of their own as Christophe Berra tumbled dramatically over a challenge by Roman Hubnik. This time, Blom booked the Wolverhampton Wanderers defender for diving. Given his earlier award, that was an odd move by the official, even if it is debatable whether the level of contact between the two players was worthy of a spot-kick either.

"There was no contact on their player and there was contact on Christophe. It's simple," said Craig Levein, the Scotland manager, whose anger was perfectly apparent.

"It beggars belief that the referee can make two mistakes of such magnitude. You will need to ask the referee why he made two such major mistakes.

" It is easy for managers sometimes to criticise referees, but when there are two decisions as stark as that, you can't say anything else other than those decisions cost us the game. I was waiting to speak to the referee but what is the point? I went to the dressing room to calm down."

It was hardly a surprise that the Czech coach, Michal Bilek, claimed ignorance. "It is difficult for me to comment," he said of the match's key decision. "From the bench, it is difficult for me to see and to judge."

Such matters will overshadow that, taking the game in its entirety, a draw was a fair result. Both teams enjoyed promising spells of possession with Scotland's lead at half-time a fortunate one.

Kenny Miller claimed the opening goal, thanks in no small measure to the ineptitude of the visiting goalkeeper Jan Lastuvka. The debutant, who was not sufficiently troubled by Scotland thereafter, made a dreadful attempt at saving Miller's routine effort.

Before that, Milan Baros had somehow fired over the Scottish crossbar from just six yards, while the Czechs had a more than decent penalty shout denied when Charlie Adam clumsily stood on Baros's foot. Already, it was clear that Blom was in for an erratic afternoon.

Driven on by excellent performances from Miller and Scott Brown, Scotland opened the second half vigorously. It is damaging, however, when teams do not capitalise on spells of superiority with goals.

The introduction of Rezek endorsed that theory. The forward crossed for Jaroslav Plasil, who used his midriff to square the game for the first time.

Hampden's silence was only temporary. Miller mugged Jan Rajnoch of the ball before supplying a terrific pass to the back post which was matched by Darren Fletcher's finish. With eight minutes to go, Scotland had hope of overhauling the Czechs in Group I.

By full time, five points still separated the countries. Scotland's best hope is that Spain and Lithuania can both defeat the Czech Republic with Levein's men also scheduled to play those nations before the qualifying campaign closes.

Scotland have made obvious progress over the past 12 months, even if they have failed to build on just a single qualification win.

"We certainly haven't given up," Levein said. "I saw a lot of things out there that really pleased me. There were so many good things, so many things that we have done in training coming off. And they showed great resilience. The group isn't finished yet, we still have an opportunity to qualify."

Next up is Lithuania's visit to Hampden on Tuesday night, a match in which anger may be as prominent in the Scotland players' minds as desire. Levein will be unable to call on Miller or Brown for that game because of suspension.

"The other team will feel like they have lost," Bilek said. Scotland have of course been here before, but his assessment was an accurate one.