Lithuania suggested that it could be a difficult evening for the hosts by limiting the space on offer in the early stages, with Jasmin Kurtic testing Emilijus Zubas with a strike from the edge of the box.
The home side improved as the first half progressed to push the visiting defence back, but chances were tough to come by as they searched for the breakthrough.
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Slovenia were gifted the opportunity to take the lead just before the break when Marius Zaliukas brought down Kurtic inside the box.
It was Valter Birsa who stepped up from 12 yards and he kept his composure to send Zubas the wrong way with the penalty.
Slovenia went in search of a vital second goal as they dominated after the interval, with Dejan Lazarevic sending an effort just over from the edge of the box.
Zubas then came to the rescue to keep Lithuania in the game with a fine save to deny Robert Beric as Slovenia threatened to run away with the match.
It was a save which proved to be vital as Lithuania claimed a point with four minutes of normal time remaining when Branko Ilic conceded a penalty for Arvydas Novikovas, who stepped up to fire past Sami Handanovic as Slovenia were left with the task of clinching their playoff spot in the final game.