There were rounds of jeers and boos from the less-than-full Hampden Park at the final whistle after a result which left Scotland in fourth place in Group A.
It took several key saves by keeper Allan McGregor to keep Scotland in the match and, although much criticised striker Kenny Miller did score, the visitors looked the more fluid and composed team.
Scotland manager Craig Levein later insisted that the result was only "a little bit disappointing" and insisted he believed the Tartan Army still supported him.
However, he conceded that his demand for a higher tempo by his players had not been entirely answered.
Scotland next visit Wales and Belgium, who last night drew 1-1 with Croatia to jointly lead the group, along with Serbia, who thumped Wales 6-1 after their 0-0 draw at Hampden on Saturday.
McGregor later admitted: "The boys didn't start well and it's hard not to start well and then up the tempo. The 15 minutes before half-time and then the second half, we improved and created chances. If we'd started with the tempo we had in the last 15 minutes of the first half, it might have been different."
He insisted Scotland's qualifying hopes remain intact despite their two-point haul up to this point but acknowledged they will face pressure.
"I know (the media) don't think so and will be caning everyone again but we believe in ourselves, it's just unfortunate we didn't get off to a good start," he said. "These aren't mugs we're playing, it's international football and every game is difficult."
Whitecaps striker Miller added: "It's not ideal, we set out to get six points and we've come away with two draws. We're bitterly disappointed because it was two home games and we've had good home form, but it's gone now.
"Saturday we felt we played well enough but tonight the performance was well below par. We need to play with a quicker tempo, we weren't up to speed in the first half and it took the goal to give us a little shake. The performance as a whole was not where we want to be and we paid the penalty for that."
Levein made three changes from the side who were held to a goalless draw against 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.
Scotland were threatening early on when Kenny Miller's cut-back found Gary Caldwell and he unleashed a left-foot 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 Nikolce Noveski.
Despite being 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 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.
At the other end, a Maloney corner found the head of Andy Webster in front of goal but the defender nodded wide of target.
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 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 would 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.
Steven Naismith later joined the fray but there was no way through for Scotland.