The two sides started slowly, with Ikechi Anya's runs down the left flank the only bright sparks in the opening minutes.
The Scots gradually grew in confidence as Barry Bannan and Anya both started to put crosses into the hosts' penalty area.
However, the first chance of the game for the visitors came only in the 26th minute when Anya swung a cross into the Macedonian box, but Steven Naismith headed it over from close range.
Pacovski was called into action again in the 44th minute when he was forced to keep out a curling effort from Anya.
Then moments later Macedonia put Scotland under pressure as Adis Jahovic hit the side-netting from a good position.