Craig Levein's men were jeered off at the full-time whistle in the Group A encounter.
There had been pressure on Scotland to deliver a win following the disappointment of Saturday's goalless stalemate against Serbia in their opener.
Kenny Miller cancelled out Nikolce Noveski's opener just before the interval but the Scots could not find a winner, leaving them with just two points from two home games in a campaign which has so far failed to live up to expectations.
The Tartan Army had hoped the football team might be able to maintain the feelgood factor in the country following Andy Murray's US Open triumph.
Instead, they were left frustrated and unhappy as the final whistle sounded, and the World Cup finals in Brazil in 2014 seemed further away than ever.
Levein made three changes to the side held by Serbia. Jamie Mackie and James Forrest, who both came off the bench on Saturday, were drafted into the starting line-up, along with Shaun Maloney.
Charlie Adam, Steven Naismith and Robert Snodgrass were the players who dropped out of the side following the stalemate at the weekend.
Adam was an injury doubt following the match against Serbia but took his place on the bench, while goalkeeper Allan McGregor played despite struggling with a recurrence of a groin problem.
Scotland were threatening early on when Miller's cut-back found Gary Caldwell and he unleashed a left-footed shot that dipped over the crossbar.
There was a warning from the visitors when Daniel Georgievski teed up the shot for Ivan Trickovski and his deflected effort fizzed just past the upright.
Macedonia took the lead after just 11 minutes in a move which began with a short corner before Georgievski was again the provider, this time for Noveski.
Despite appearing to be in an offside position when the ball was played, the flag stayed down and Noveski stabbed home past McGregor from close range.
Boosted by the early opener, Macedonia went searching for a second goal and Agim Ibraimi drove just wide of target from long distance.
There was concern for Scotland when McGregor appeared to come off worse following a collision with Mirko Ivanovski, but he was able to continue after treatment and quickly came to the rescue to deny Ibraimi.
Maloney was then fouled just outside the box by Muhamed Demiri but his subsequent free-kick was comfortably dealt with by goalkeeper Martin Bogatinov.
Scotland hauled themselves level two minutes before the break when Mackie delivered an inviting ball across the face of goal and Miller fired home into the gaping net from close range.
Macedonia looked dangerous after the re-start and Christophe Berra had to react quickly to block a Georgievski effort, before Ferhan Hasani rattled the right post with a powerful curving shot.
Levein made his first change with just under an hour on the clock and Miller was withdrawn for Adam to boos from the crowd, who perhaps wanted to see the introduction of Jordan Rhodes instead.
Mackie took over from Miller as the lone forward but chants of 'We want a striker' rang around the stadium as Scotland searched for the goal that might set them on their way to a win.
Rhodes was thrown into the action for James Morrison after 66 minutes and immediately saw his diving header fall agonisingly wide of the post from an Adam cross.
Macedonia provided a timely reminder of the threat they still posed when Ivanovski found himself through on goal but McGregor was up to the task with a superb save.
There was another opportunity for Rhodes but the Blackburn striker was unable to connect properly at the back post after throwing himself in front of a Forrest cross.
Naismith replaced Mackie as the Scots made a final push for the three points, but it was McGregor who was called into action again to smother from Goran Pandev late on.
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