Scotland needed victory to secure second place in qualifying Group F, with the understanding rivals Slovakia would beat Malta.
But a Roman Bezjak header cancelled out Leigh Griffiths’ opener before the Rijeka loanee scored again to end Gordon Strachan’s hopes of securing a playoff spot.
Robert Snodgrass scored at the death but it wasn’t enough.
With England already confirmed as group winners, the battle for second place was on.
Scotland took the lead through Griffiths’ well-timed shot into the bottom corner and could have gone further ahead before the break.
But Slovenia, who themselves could have mathematically secured second place had Slovakia not won tonight, had other ideas.
Bezjak crept up at the far post to nod in a soft goal on 51 minutes and raise the hosts’ spirits.
And Slovenia deservedly took the lead when Bezjak inexplicably side-footed home from 12 yards unmarked in the box from a corner.
Darren Fletcher had a golden chance to level with 12 minutes remaining but volleyed over inside the box.
Snodgrass then bundled home a leveller on 87 minutes and the Scots then almost snatched the three points moments later.
Bostjan Cesar still had time to be sent off for a straight red card as the Scots bombed forward.
But it was far too little too late for Scotland, with boss Strachan now facing the axe after another qualifying failure.
Full report to follow…