After defeat in Serbia on Friday night, this stalemate leaves their prospects of qualifying for the finals in dire straits despite having lost only one of their five games.
Chris Brunt was almost the hero for his side but the West Brom man fell agonisingly short of of converting Corry Evans' cross in the 80th minute.
Nigel Worthington's men were second best for much of the game as they lost the ball cheaply throughout, but had the two best chances of the match through Brunt and Gareth McAuley.
In the sixth minute Josip Ilicic tried his luck when he lashed a loose ball at goal from 25 yards.
Lee Camp, on his home debut, was well placed but fumbled the ball. Luckily for Northern Ireland, there was nobody following up for Slovenia.
Marko Suler followed Ilcic's lead moments later, striking from the edge of the area but this time Camp held on safely.
There was a moment of hesitation in the Slovenia box soon after, Grant McCann almost taking advantage of some confusion between Samir Handanovic and Miso Brecko.
A clever touch by Brunt released Warren Feeney on the counter attack but he narrowly failed to pull away from his marker as he charged toward goal.
With 20 minutes gone Sammy Clingan lost possession in a dangerous area, allowing Armin Bacinovic to showcase some neat footwork before laying the ball to Valter Birsa.
His shot tested Camp again and the Nottingham Forest man was able to tip over the bar.
Northern Ireland were looking short of ideas up front, too frequently surrendering possession after playing high balls to Feeney.
Slovenia were a little more composed, with Birsa dangerous in attack, and the crowd were growing restless the more the visitors retained the ball.
Ilicic limped off after 29 minutes, replaced by Gent's Zlatan Ljubijankic.
Finally, four minutes before the interval, they managed their first attempt on goal.
It was a good one too, Clingan lining up a free-kick from 20 yards and sending it just wide of the post with the Handanovic beaten.
Feeney re-emerged with a bandaged head after receiving four stitches following a knock in the first half.
Things almost took a turn for the worse in the 49th minute, Milivoje Novakovic shooting over after meeting a crisp low cross eight yards from goal.
Corry Evans almost created something out of nothing when he charged down a lost cause in the Slovenia area, but the midfielder's exuberance earned him a yellow card seconds later.
Suler went close when he latched onto Andraz Kirm's cross at the near post, heading into the side netting to Camp's relief.
McAuley, captain for the day in Aaron Hughes' absence, was in fine form at the back, twice making last-ditch slides to end dangerous moves.
That he needed to do so reflected Slovenia's growing confidence.
With the game apparently getting away from Northern Ireland, McAuley almost made his mark at the other end for the second time in a week.
Having scored the opener against Serbia, he met McCann's hanging free-kick at the far post and nodded to towards goal.
Handanovic was out of the picture but Matej Mavric was on hand to clear off the line.
With 20 minutes remaining Worthington sent on Millwall forward Josh McQuoid, winning his second cap and slotting in on the left flank.
McQuoid was quickly into the action, getting on the end of Corry Evans' cross but failing to test the goalkeeper.
As the game entered the last 10 minutes, the home side produced their best move of the match.
Jonny Evans played a fine cross-field ball to his brother Corry on the right and he laid it back across goal first time with a neat touch.
Brunt raced to meet it inside the six-yard box but the ball agonisingly brushed his boot and crept to safety.
There was time for Camp to make a fine save from Zlatko Dedic and for McQuoid to make an unsuccessful penalty appeal but in the circumstances the result still felt like defeat.