After a tense opening period, Leigh Griffiths pounced on a ball over the top by James McArthur and the Scotland striker hammered a low shot into the net to give his side the lead on 32 minutes.
However, Slovenia got back on level terms early in the second half as a free kick was met by the head of substitute Roman Bezjak to make it 1-1.
And it was Bezjak who put his side ahead as he coolly slotted home after a corner fell to him inside the box. Darren Fletcher missed a great chance to equalise with a shot over the bar, but Robert Snodgrass did brilliantly to control a cross and level the scores with a hooked finish.
In the end, though, it was not enough as Scotland could not find a winner even after the late dismissal of Bostjan Cesar. As a result, Slovakia moved up to second place after beating Malta 3-0 -- thanks to two goals from Adam Nemec and one from Ondrej Duda -- but the result may not be enough to seal a spot in the playoffs as they are currently UEFA's worst runner-up and can only qualify if Wales or Croatia draw.
In Group F's other game, already-qualified England gave debuts to Harry Winks and Harry Maguire and came away from Lithuania with a 1-0 win. Harry Kane converted a penalty in the 27th minute after Dele Alli was brought down in the box.
And, with Jack Butland forced to make a fine save to keep them ahead, England created little else yet rounded off the qualifying group unbeaten. In Group E, Poland ensured their place at the World Cup with a nervy 4-2 win against Montenegro.
Poland went ahead early on with a goal from Krzysztof Maczynski in the sixth minute and Kamil Grosicki doubled the lead shortly afterwards. But a remarkable comeback saw Stefan Mugosa and Nikola Vukcevic hit back before Robert Lewandowski struck and a Filip Stojkovic own goal made sure of all three points.
Denmark took their place in the playoffs after a 1-1 draw against Romania ensured they finished second on 20 points. Christian Eriksen continued his fine form with a penalty and, shortly after, Cristian Ganea was handed a second yellow card. But Ciprian Deac struck with an 88th minute leveller.
In the final group game, Kazakhstan drew 1-1 with Armenia -- with both sides long since out of contention for a place in the finals.
Manchester United midfielder Henrikh Mkhitaryan got himself on the scoresheet with a delightful chip but Bayurzhan Turysbek struck a 61st minute equaliser.