Marc Janko fired the hosts into a 16th-minute lead but Marius Stankevicius levelled for the visitors after 66 minutes.
However, Wallner stepped up to confidently stroke in the winner from the spot after Franz Schiemer was brought down in the penalty area.
It was Austria's fourth win of the qualifying campaign as they ensured a third-placed finish behind Serbia and France.
The hosts opened the scoring with the first real chance of the game.
Defender Schiemer found Janko, who surged into the area and drilled the ball into the top corner.
Nine minutes later Wallner's free-kick caused problems in the visitors' defence.
Lithuania goalkeeper Zydrunas Karcemarskas cleared with his fists and Austria midfielder Yasin Pehlivan picked up the ball, but could not find the target.
Wallner attempted to lob Zydrunas Karcemarskas but the goalkeeper saved well.
Lithuania's first opening came in first-half stoppage time, but Schiemer cleared the danger after Edgaras Cesnauskis' shot.
There was still time for Veli Kavlak to get a shot away, but he fired over.
Lithuania were more aggressive early in the second period and were rewarded after 66 minutes.
A left-wing cross from Cesnauskis was converted by Stankevicius, tucking into the bottom corner from the centre of the area.
Stefan Maierhofer had a header cleared off the line before Schiemer was brought down in the box by Vidas Alunderis.
Wallner sent Karcemarskas the wrong way from 12 yards to restore Austria's lead, but there was still a moment of concern when Tomas Danilevicius had a shot blocked before the victory was sealed.