A Euro 2012 qualifying place was Scotland's if they matched the Czech Republic's result in Lithuania but, as the Czechs won, Scotland lost.
"They're unplayable," Naismith told BBC2 after the game.
"They move the ball so quickly, it's hard to track the ball. We could have defended a little better but that's why they're world and European champions.
"We tried to get forward as much as we can, but when they had possession we couldn't get into them as they'd carve us open.
"But over 90 minutes and two games against them, we showed up well and scored three goals."