Going into the round Craig Levein’s men held second place, ahead of the Czechs by one point.
However, the Tartan Army knew that their side would have to match Czech Republic’s result to ensure a playoff berth, but this was a bridge too far against an impressive Spain team.
Manchester City midfielder David Silva scored a brace in the first half to give the hosts a comfortable 2-0 half time lead, with Barcelona attacker David Silva piling on the misery with a third early in the second period.
David Goodwillie did manage to get a consolation goal for Scotland from the penalty spot, but in the end the celtic nation were outclassed by the world champions.
Despite the defeat, Levein praised his players in what was always going to be a difficult task for Scotland.
“The result is disappointing. We don’t like to lose but as I said to the players after the game, this is as hard as it gets,” he stated to BBC Sport.
“To come to the home of the European and world champions, play them in their own backyard, is an extremely difficult thing to do.
“We knew we had to be at the top of our game and they maybe would come down 10 or 15 per cent – well, unfortunately for us they played pretty close to maximum tonight. When they are like that they are very difficult to play against.
“I have to give credit to our guys though, they stuck at it in the second half and on another night could have had three or four goals,” he concluded.
Czech Republic will now wait to find out their playoff opponents in their continued attempt to make the finals in Poland and Ukraine, whilst Scotland will look to regroup before World Cup qualifying begins.
Scottish fans will look back to the 2-2 draw with Czech Republic at Hampden, with a controversial late goal by the visitors ultimately costing Levein’s men a place in the playoffs.
By Gareth McKnight