Craig Levein's side went in to the game requiring victory over the world and European champions to guarantee second place ahead of Czech Republic, although matching the Czechs' result in Lithuania would have been enough.
However, neither scenario unfolded, with the Scots being swept aside 3-1 - as most people outside the Scottish camp predicted - while Czech Republic cruised to a 4-1 win in Kaunas.
Adam admits the damage to the Scots' qualification hopes was done before they arrived in Spain.
But he will take encouragement from aspects of the performance against the all-conquering Spanish - who won all eight qualifiers - into the 2014 World Cup qualification campaign which begins next year.
"If we are honest with ourselves we left it too late," he said.
"It's tough going to places like Spain and trying to get three points.
"They are the world champions and it is difficult.
"But you have to take the positives. We created chances and scored a goal.
"I think we will be a better team when the qualifiers for Brazil come around."
Scotland finished in third place with 11 points from eight games - two less than the Czechs, who collected four points from the two games between the countries.
Adam concurred with Levein's post-match claim that Scotland would have fared better in the campaign had he had more time to prepare for it.
"We changed a number of players during the campaign but we have had a settled squad for the last four or five games," said the former Rangers player.
"It was difficult but I think we did well enough.
"We are disappointed not to get to the play-offs but, as I said, we left it too late."
For whatever reasons, the Scots have once more come up short in a qualification campaign.
Scotland have not qualified for the finals of a major tournament since the 1998 World Cup in France.
Adam will not relish another football-free summer next year when the cream of Europe will be playing against each other in Ukraine and Poland.
"It is hard to take," the 25-year-old said.
"But we will evaluate everything that happened and sit down as a group of players and see where we can improve and that's the way forward if we want to become a better team.
"You've seen last night [Tuesday] that we can pass, move and create chances.
"We now have a squad who is close together and we are looking forward to the future.
"There will be plenty of friendlies before the next qualification campaign begins so the players will go back to their clubs and try to play as well as they can and try to get back in the Scotland squad for the next match."