With a tense match petering out towards a goalless draw, Kolarov delivered a trademark thunderous left-footed strike between the legs of goalkeeper Berisha at the end of a stoppage time counter-attack.
Adem Llajic made sure of the three points with another goal on the break two minutes later to give the away side a famous victory.
One year on from their meeting in Belgrade which was abandoned due to a drone helicopter bearing a controversial banner, Albania and Serbia resumed their footballing rivalries in Elbasan.
Kolarov had acted as peacemaker on that occasion, helping to curtail the unsavoury scenes which followed, in what is one of the continent’s most politically charged clashes of recent years.
Happily, matters on the field took precedent this time and Serbia had the better chances in the first 45 with Ljajic closest to breaking the deadlock before the interval.
The Inter forward had the ball in the back of the net via at least one deflection but the Italian official ruled it out for offside – correctly, as replays showed.
Albania, who knew they could book their place at their first major tournament if they could better Denmark’s result against Portugal, had their chances and dominated possession, but the visitors always carried the greater threat on the counter.
Serbia, rooted to the bottom of Group I, were playing solely for national pride, and that’s exactly what they restored – although their supporters would have to be patient.
Four minutes of additional time were added on at the end of the 90 and that’s when Kolarov came up with the goods – a rocket of a strike to break the deadlock from an acute angle.
Llajic put the gloss on the scoreline with his chip over the onrushing goalkeeper in the final minute to give Serbia a first win of the campaign.
Meanwhile in Nice, Euro 2016 hosts France entertained Armenia in an international friendly which Bacary Sagna was named in the starting XI for and Eliaquim Mangala started on the bench.
Atletico striker Antoine Griezmann gave Didier Deschamps’ side the lead ten minutes before the break, before Karim Benzema netted twice and Yoann Cabaye scored another in the second 45.
Sagna played the full 90 minutes for France, while Mangala, only just back from his injury lay-off, remained an unused substitute.
