The on-loan Fulham striker cashed in on defensive lapses in the 68th and 81st minutes to inflict on the Eagles their second defeat under manager Gernot Rohr, as the three-time African champions put up an underwhelming performance in London.
Both sides had contrasting fortunes in their last friendlies with Nigeria beating Poland 1-0 while the Serbs lost 2-1 to Morocco.
Rohr made four changes to the starting line-up against Poland with Nantes defender ChidozieAwaziem coming on as a late replacement for Leon Balogun, who failed a fitness test.Ogenyi Onazi, Tyronne Ebuehi and Ahmed Musa, all substitutes against the Polish, started against the Serbs.
Captain Mikel Obi also missed this tie due to work permit issues in China and it was glaring that the Eagles struggled in the middle of the pack as Leicester man Wilfred Ndidi, Onazi and Torino midfielder Joel Obi failed to blend in the midfield.
Nigeria’s Francis Uzoho was the busier of both keepers in the early stages and he managed to stop Mitrovic’s fierce drive from outside the box as early as the eighth minute.
However, the Eagles almost took an unlikely lead when Victor Moses turned swiftly before shooting a low angled shot but Vladimir Stojkovic, in goal for Serbia, parried for a corner.
The Serbians should have been ahead after then, when Uzoho fumbled Mitrovic’s header inside the six-yard box. The Deportivo La Coruna keeper managed to recover the ball back but replays showed the entire ball had crossed the line.
Dusan Tadic should have put the Europeans ahead after being put through just before the break, but the Southampton midfielder watched his rasping drive hit the side netting with Uzoho beaten.
With the Eagles failing to strike a rhythm after the break, the Serbs increased the pressure and they always looked like the side likely to score. And they did in the 68th minute when Mitrovic grabbed his first goal of the night after some awkward defending by the Nigerians.
Mitrovic then stroked the ball into an empty net in the 81st minute after some good work on the flanks by Dusan Tadic to silence the pockets of Nigerian fans at the stadium.
China-based striker Odion Ighalo, who came on for Moses, tried to add some spark to the Eagles’ attack while Rohr introduced John Ogu and Mikel Agu to add some steel in the midfield but they were unable to solve the team’s midfield problems.
The defeat meant Serbia ended Nigeria’s five-game unbeaten run of matches played in London, since a 1-0 defeat against Australia in November 2007.