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 and Adam said: "If we are honest with ourselves we left it too late."
He added: "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."
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Source: PA