The home team got off to a tepid start and fell behind when Nikolce Noveski slid home the opener after 11 minutes.
Scotland finally found a rhythm around 25-30 minutes in and draw level in the closing stages of the first half through Kenny Miller.
But the buzz of finally scoring their first goal of the qualifying campaign was not enough to push them on to turn the score on its head despite the second-half introduction of Jordan Rhodes, and they have goalkeeper Allan McGregor - who only passed a fitness test on the day to start - to thank for a string of excellent saves which prevented them falling behind a second time.
Two points from two home fixtures Scotland could, and should, have won leaves them behind early pace-setters Serbia, Belgium and Croatia in Group A, all with four points apiece.
With confidence among Scotland supporters low and the 0-0 qualification opener at home to Serbia doing little to change that, Craig Levein was in desperate need of a lively start to relax some of the nerves surrounding the blue shirts.
It did not come: the hosts took an age to find their feet in the contest and by the time they did, they were behind to Noveski’s conversion of a cross from the left following a short corner routine.
McGregor denied the men in red a second on the half hour mark after Napoli’s Goran Pandev was put clean through, but from there Levein’s troops began to slowly shake off the pressure and make good on their superior possession.
Shaun Maloney had a wicked free-kick strike from just outside the box swatted away by Martin Bogatinov in the Macedonia goal, while James Morrison and James Forrest tormented the back line with a series of tantalising balls into the danger zone.
The breakthrough came with two minutes to spare in first half regulation time as the visiting defenders switched off and allowed a Morrison through pass reach Jamie Mackie, whose square pass offered Miller a simple tap-in for 1-1.
Left-back Paul Dixon showed Scotland’s intent had not been diluted by the interval with a decent low drive which was well held by Bogatinov a few minutes into the half, but just before the hour mark McGregor had to be in fine form to deny Daniel Georgievski and substitute Ferhan Hasani.
The introductions of Rhodes and Charlie Adam coincided with another stepping up of the tempo from the hosts and the £8million Blackburn recruit almost made an immediate impact with a close range diving header from his fellow replacement’s driven cross.
With 18 minutes remaining, Pandev supplied one of many cultured through passes into the Scotland area to put Mirko Ivanovski clean through only for McGregor to get a leg to his attempt to square to Agim Ibraimi in a similar scene to that of Scotland’s leveller.
And with moments remaining it was again Macedonia coming closest to snatching a winner with Ibraimi squaring for Pandev to force yet another stop from McGregor.
The match pulled Scotland's lowest home attendance for a qualification fixture in 11 years and on the evening's evidence, numbers are not going to experience a sharp rise any time soon.
Belgium recovered from conceding an early goal but failed to capitalise on their second-half dominance in a 1-1 draw with Croatia in an open and fluid match.
The home side, narrow bookmakers' favourites to win Group A despite their lowly 40th world ranking, fell a goal behind in the sixth minute, equalising on the stroke of halftime before neat footwork created chances but not goals.
Croatia's Ivan Perisic drove in an easy opener when Vincent Kompany failed to fully clear Darijo Srna's cross.
Belgium's Guillaume Gillet, the sole home starter still playing for a Belgian club, thundered in an equaliser from a half-cleared corner in the final play of the first half.
Belgium talked before the match of shutting down Croatian midfielder Luka Modric, but it was wingers Srna and Perisic and the imposing Mario Mandzukic in the centre who threatened most.
In the other Group A match, Serbia thrashed Wales 6-1 to leave Chris Coleman's side pointless and bottom of the table.