Naismith fired the only goal on 50 minutes, moving into space to rifle Barry Bannan's teasing cross high into the net at Hampden Park.
The hosts, denied three points at home on Saturday when Czech Republic earned a 2-2 draw with a last-gasp penalty, were awarded a spot-kick of their own when Tadas Labukas inexplicably handled a cross just before half-time.
The Scots failed to capitalise though, Zydrunas Karcemarskas diving to his left to save Darren Fletcher's penalty.
Scotland dominated for long periods but could not add to their lead.
They stayed third on eight points after six games, two behind Czech Republic. Spain lead the group.
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