Gordon Strachan's side claimed only their second win in the current qualifying campaign after a 2-1 victory over Macedonia in the Balkans, however they left it late in Skopje to seal all three points.
It was a slow opening half as neither side was able to break the deadlock. However Scotland looked more likely to do so as they looked to control possession early on, though a poor playing surface made passing rather difficult.
Glasgow born Ikechi Anya - making his full debut after appearing as a substitute in Friday night's defeat to Belgium - looked like Scotland's biggest threat, so it was no surprise that his teammates constantly looked to shift the ball out wide to him. Anya created the first real chance of the game when his pin-point cross found Steven Naismith but the Everton striker couldn't keep his header down.
Just minutes later it was Naismith who would be the creator after his long ball over the top of the Macedonia defence fell to skipper Scott Brown but his effort was too close to Pacovski - between the sticks for Macedonia.
The hosts found themselves with a fantastic chance to take the lead not long before the break, unfortunately for them Jahovic could only blast the ball off of the side-netting following Trickowski's defence-splitting pass, timed to perfection.
A moment of comedy at the restart - referee Fredy Fautrel signalled for the restart without noticing that Jahovic hadn't returned to the pitch and upon realising this he had to stop play.
The away side - who had to substitute their goalkeeper at the break as Matt Gilks replaced the injured David Marshall - didn't see much of the ball at the beginning of the second half.
Just before the hour mark though, man of the match Ikechi Anya fired Scotland into the lead from a tight angle - his first goal for the nation of his birth. Some questionable goalkeeping perhaps though there were no complaints from the Scotland players.
Both teams began to up the tempo following Anya's strike as the home side began to attack more as they pressed for an equaliser. They forced Blackpool stopper Gilks into a few diving saves, the best chance arguably fell to substitute Ivanovski.
It looked like Strachan's men would remain rooted to the bottom of the group table seven minutes from the end when Jovan Kostovski looked to control a high ball in the box, his first touch took the ball past Gilks - although it didn't seem intentional - before tapping it in with his second.
On the 88th minute Shaun Maloney won a costless-kick on the edge of the area, of which he assumed the responsibility. The Wigan midfielder curled the ball beautifully into the top corner giving the goalkeeper no chance and sent the Tartan Army into raptures.
There wasn't enough time for Macedonia to find a way back into the game as Scotland took the three points back to Hampden, as they continue to progress under new manager Gordon Strachan, so far winning three out of five games under the former Celtic and Middlesbrough boss. His side are now leapfrog both Macedonia and Wales at the bottom of the table after the latter were defeated at home to Serbia.
