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Albania continued to put pressure on the Serbia goal when Taulant Xhaka raided forward and fired an effort on target, but Stojkovic made the save.
Lila had another strike at goal just before the break following a well-worked move by the hosts, but he curled his effort over the bar from a tight angle on his left foot.
In the second half, Serbia came out with an attacking intent and Luka Milivojevic seized the ball and drove towards the final third. The midfielder was not closed down by the Albania defence and opted to shoot for goal, but his strike sailed over the bar.
The hosts managed to get back on the front foot when Emir Lenjani tested the handling ability of Stojkovic, but the keeper was equal to the effort to keep the scores level.
Serbia broke the deadlock late in the game when Kolarov brought the ball forward down the left and crashed an effort across Etrit Berisha to find the bottom corner.
The visitors secured their win in the 94th minute as they hit Albania on the counter and Ljajic finished well by lobbing the ball over Berisha into the net.
The defeat leaves Giovanni De Biasi's men in need of a positive result in their final game to have any chance of earning automatic qualification from Group I.