Scotland's chances of qualifying for World Cup 2014 hang by a thread after just two matches following a second home draw in four days.
Macedonia's early goal by Nikolce Noveski should have been chalked off for offside, but they were good value for the lead.
Kenny Miller levelled before the break having been set up by Jamie Mackie.
Both sides had chances to win, with Macedonia hitting the post and forcing Allan McGregor into several good saves.
Arguments may be made about there still being plenty of points to play for.
But, on the evidence of the games so far, Scotland will not be going to Brazil in two years' time.
Miller and Morrison celebrate after Scotland's equaliser at Hampden Park
The home side did fashion the first chance of the match, but Gary Caldwell's left-foot drive was never in danger of threatening Martin Bogatinov's goal.
Conversely, Ivan Trichkovski's drilled shot from 10 yards just a few moments later had McGregor scrambling to turn it wide.
Macedonia took confidence from that and, when Trichkovski fired the ball across goal and Noveski, who was a yard offside, directed it past McGregor from six yards to give Macedonia an 11th-minute lead.
Scotland were rattled and, unlike their more technically adept opponents, were unable to string more than a couple of passes together.
Agim Ibraimi came within inches of inflicting further grief on the home side, as his shot on the turn flew close.
McGregor again bailed his side out as they were caught on the counter-attack and, although there was a whiff of offside, Ibraimi was allowed to shoot, only for McGregor to block superbly.
Shaun Maloney and Mackie tried their best to drag the Scots up by their bootlaces, with both players busy and energetic.
A Maloney corner was headed just wide by Andy Webster on the half-hour mark before Bogatinov was forced to punch away a powerful free kick by the Wigan player.
As half-time approached, Scotland at last began to build some momentum, with James Forrest also springing to life.
It was James Morrison who managed to squeeze a ball past Vanche Shikov through to Mackie, who showed supreme selflessness to square for Miller to tap into the empty net.
Interview - Scotland manager Craig Levein
The Scots began to display a vigour that had been absent previously and Paul Dixon tested Bogatinov with a low drive from long range at the start of the second half.
Scotland were certainly more of an attacking threat by this stage, but Macedonia still looked the likelier side to score and Ferhan Hasani hammered a shot off McGregor's left-hand post from just outside the box.
Charlie Adam replaced Miller and then the Hampden crowd got the substitution for which they had been clamouring as Jordan Rhodes came on for Morrison and the pair almost combined to immediate effect.
However, the striker's flashing header at the near post from Adam's cross found only the side-netting.
McGregor continued to show his worth as he rushed out to deny Mirko Ivanovski, who had been played in by a deft pass from the left boot of the majestic Goran Pandev.
By the closing 15 minutes, Macedonia were content to take a point and Bogatinov was largely untroubled as they managed that relatively comfortably, much to the chagrin of the home support.
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