Michael O'Neill's men could still make it to the US next summer if they qualify through the play-offs
The nation went down 1-0 against Slovakia in Kosice on Friday evening which ended their chances of making it out of their qualifying group but have been assured of a play-off place regardless.
Tomas Bobcek, who was making his debut for the Slovaks, had only been on the pitch for three minutes in when he fired in during first of eight minutes added on.
The goal controversially stood despite Northern Ireland appeals for a foul after Daniel Ballard had gone down in the build-up.
Northern Ireland, missing four of the players who started last month against Germany, battled hard for 90 minutes but Slovakia held the edge and will go to Leipzig on Monday with a chance to top the group if they can beat Germany.
Their misery was completed by a second yellow card for Ballard in the dying moments, but Croatia's 3-1 win over the Faroe Islands means they will be in the play-offs in March having won their Nations League group.
After a shaky start, the visitors grew into the game and should have led 17 minutes in when Ballard beat three defenders to get his head to Justin Devenny’s free-kick, only to see his chance go a whisker wide.
Slovakia thought they had taken the lead eight minutes into the second half when Haraslin’s drilled low free-kick from a tight angle went all the way through, but Milan Skriniar was offside as he stretched for the ball in front of Peacock-Farrell.
That raised the volume levels inside the Kosicka Futbalova Arena and they were even louder ten minutes later when the hosts had another one ruled out.
O'Neill tried changes of personnel and shape but Slovakia kept on coming and the resistance broke at the death as Peacock-Farrell was unable to deal with the corner and Bobcek had his moment of glory.
Ballard was then shown a second yellow for a push on Lobotka to earn his marching orders and, as the night unravelled for Northern Ireland, O'Neill was also booked by referee Istvan Kovacs after the final whistle.
