Macedonia recorded their first win in World Cup qualifying - a result which left visitors Serbia six points behind Group A pace-setters Belgium and Croatia.
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Agim Ibraimi scored the only goal with a second-half penalty after Serbia's Nenad Tomovic was sent off.
Serbia were flat in attack and were unable to break down the home defence, while full-back Aleksandar Kolarov was wasteful from set-pieces.
Dusan Tadic shot wide for Serbia in the second minute before Boban Grncarov tested visiting keeper Zeljko Brkic.
Manchester City's Kolarov shot wide three times in quick succession, while Mirko Ivanovski's curler at the other end was also off target.
Two minutes into the second half, Kolarov tried to catch out Brkic direct from a free-kick in his own half, but the keeper was alert to the danger and saved.
Macedonia went ahead in the 58th minute when Tomovic hacked down Ivanovski in the penalty area and was shown a straight red card, and Ibraimi slotted the ball low inside the left post.
Milan Bisevac's block prevented Ferhan Hasani doubling the home side's lead in the 67th minute, but Serbia were struggling to create chances of their own.
Zoran Tosic saw a cross cleared by Ivanovski and then sent a poor shot soaring over the crossbar.
Aleksandar Ignjovski went closest to an equaliser with five minutes remaining when his drive from the edge of the box was well saved by Macedonia keeper Tome Pacovski.