Billy Stark's side had to win their last two remaining games in Senec last night and in Luxembourg on Monday to have any chance of finishing second in their group. But in truth, it would have needed an improbable mathematical miracle anyway because of an inferior goal difference.
However, in a campaign of disappointments and some heavy thumpings, Scotland produced a disciplined, determined display that almost secured an unlikely win until a 90th-minute equaliser from Ondrej Duda. It was particularly disappointing for goalkeeper Jordan Archer, who produced a series of great saves.
Stark admitted he was disappointed at not securing a rare win. He said: "It was heart-breaking. Looking at this campaign you're searching for that wee bit of luck at the right time. We've never really found that.
"But the performance the players put in tonight deserved a victory. They got back the determination and resilience to defend properly against a good side with a real presence.
"We countered intelligently and created good chances. There were lots of good individual displays but collectively they really showed they were a team. With a young group we can take a lot of heart. You don't get ahead of yourself but the midfielders showed they could do both parts of the game well.
"We'd trained to get Ryan Fraser and Stevie May through on them and that happened on numerous occasions. We can improve on focusing on the game - not just thinking about playing - but on how the team functions and what can work for us."
Stark made five changes from the side that were thrashed in their last game at home by the Netherlands in May. Ryan Gauld, Craig Slater, Clark Robertson, Lewis Macleod and Ryan Jack all started at Slovakia's National Training Centre last night. Gauld may be a Sporting Lisbon superkid these days, but he was bizarrely listed on the team sheet as playing for East Fife and with the wrong surname.
The home side were also boosted by the news that the Dutch had surprisingly lost at home earlier to Georgia, which meant a win last night would put them level with the Netherlands at the top of the group and it took a superb block by Celtic's Stuart Findlay to prevent Slovan Bratislava's David Hudak's close-range shot from giving Slovakia the lead.
The Scots looked dangerous on the counter attack and Fraser embarked on an exciting run from his own half into the home side's box before teeing up Gauld. But the former Dundee United midfielder was closed down, his shot was deflected for a corner.
Scotland suffered a blow midway through the half when Aberdeen full-back Clark Robertson limped off with a thigh injury. Robertson had only just come back from a long-term knee injury too, although Stark revealed after the game it was nothing too serious. He was replaced by Hamilton's Stephen Hendrie, who made his under-21 debut.
Tottenham's Archer then kept the young Scots in it when he brilliantly clawed away a fierce shot from the edge of the box from Duda.
The Ukrainian referee Anatoli Zhabchenko then had to stop the game for another injury . . . to himself. He limped off clutching his calf and was replaced by fourth official Sergil Lysenchuk.
The Slovakia striker Adam Zrelak should have given his side the lead when he volleyed over from close range, with the Scots screaming for an offside call that never came.
Scotland stunned their hosts with the breakthrough thanks to a fantastic counter-attack. Macleod split the Slovakian defence with an exquisite pass to release Fraser, who coolly rounded the goalkeeper before tapping the ball into the empty net from an angle.
Archer made a series of saves as the Slovaks desperately pressed in search of an equaliser and they scored when Duda finally beat Archer with a low drive.