Nigel Worthington saw his side give a lung-bursting display in the Slovakian sun but they had nothing to show for their efforts at the end of it.
Instead the province were again left to reflect on an opening-day defeat in a qualifying campaign.
This is the the fourth time in a row they have started with a loss, although it was close-run thing on Saturday evening.
Goals from Martin Skrtel and Marek Hamsik put Slovakia in the driving seat before Northern Ireland were thrown a lifeline in the 81st minute.
Jan Durica diverted a cross from substitute Chris Brunt into his own net but that was as good as it got for Worthington's side.
Northern Ireland made a bright start and David Healy stated his intentions as early as the seventh minute when he tried his luck on goal, only to see his effort deflected to safety.
Then a minute later Sammy Clingan sent a 20-yard shot into the body of Slovakia goalkeeper Stefan Senecky.
The hosts again found themselves on the back foot when Chris Baird got on the end of Keith Gillespie's corner but headed wide.
The home crowd screamed for a penalty after 13 minutes when Martin Jakubko went down under a challenge from Stephen Craigan but the referee would have none of it.
The province's tactics were quite clear and they tried to release Healy at every available opportunity.
Slovakia thought they had taken the lead two minutes later when Jakubko found the corner with a glancing header. However, his effort was ruled out for offside and Northern Ireland breathed a sigh of relief.
There was another scare for Worthington in the 39th minute when goalkeeper Maik Taylor flapped at a long ball and almost diverted it into his own net. In the end he was just grateful to concede a corner.
Healy almost put them ahead two minutes from half-time when his effort went beyond Senecky but narrowly wide of the post.
Northern Ireland were rocked in the 46th minute and found themselves a goal down.
Skrtel peeled away from his marker and headed the ball beyond Taylor following a curling free-kick from Marek Sapara.
It was body blow for the province given how assured they had been in the first half.
However they hit back and George McCartney got on the end of a corner from Gillespie, only to head high over the crossbar in the 50th minute.
Gillespie, who had been troubled by an ankle injury, then came off and Warren Feeney was drafted into the action.
Martin Paterson then surged forward only to send his shot into the goalkeeper's arms after 64 minutes.
Slovakia were suddenly looking uncomfortable and Senecky flapped at a cross from Aaron Hughes after 66 minutes.
Worthington switched things around a minute later, bringing on Brunt for Paterson, who had put in a hard shift.
Northern Ireland then had loud appeals for a penalty dismissed after a shot from Baird appeared to be handled in the 69th minute before the home side doubled their lead through Hamsik.
Brunt tried his luck from distance in the 80th minute but his effort flew high over the crossbar.
A minute later Northern Ireland grabbed a lifeline thanks to an own goal from Durica, who diverted a cross from Brunt into his own net.
Feeney almost equalised on the stroke of full-time only for Senecky to claw the shot over the crossbar before smothering McCartney's effort.