Four days after securing their place in South Africa as Group Seven winners, the Serbians were beaten by penalties from Mindaugas Kalonas and Marius Stankevicius. Zoran Tosic netted the visitors' reply, but it was not enough to prevent a second defeat in their pool.
On a soggy night in Lithuania, the home side seemed to cope better with the conditions - and Serbia goalkeeper Vladimir Disljenkovic made several early saves to keep their opponents at bay. However, he was eventually beaten after 20 minutes when Neven Subotic was punished for a challenge in the area on Ignas Dedura.
Kalonas stepped up to take the resulting penalty, with the wet ball slipping under the hands of Disljenkovic. Serbia showed more promise at the start of the second half, and the arrival of substitute Tosic soon brought them back on level terms.
The Manchester United man was able to weave a path through the Lithuanian defence after 59 minutes, before rounding goalkeeper Zhidrunas Karchemarskas and slotting home. The home side responded with a wave of attacks and regained the lead again from the spot after 68 minutes.
Udinese defender Aleksandar Lukovic, another substitute for Serbia, was adjudged to have clambered illegally over Kalonas while attempting to reach a header - prompting Bulgarian referee Anton Genov to point to the spot. This time it was captain Stankevicius who stepped up to the mark, making no mistake.
Serbia, without several regular starters such as captain Dejan Stankovic and Nemanja Vidic, pressed hard for a point. However, luck was not on their side as first Branislav Ivanovic hit the post after 73 minutes and Mindaugas Panka cleared a Tosic shot off the line in the dying stages.