The loss in Kosice does damage their hopes of making it to North America, however, as they will enter those play-offs among the fourth group of seeds.
Slovakia originally thought that had taken the lead in the 56th minute when Lukas Haraslin’s free-kick flew past Bailey Peacock-Farrell, but it was adjudged that Milan Skriniar had obstructed the view of the Northern Ireland stopper.
Just eight minutes later, they had another strike disallowed by VAR after David Strelec was penalised for handling the ball.
O’Neill felt that the decisions to disallow the previous efforts played into allowing the late winner.
“It was a clear push on Daniel Ballard at the corner, two hands in his back,” said O’Neill.
“The other goals that were disallowed should have been disallowed. The first one was offside, the lines show that clearly and the second one was handball.
“You have to look at each incident in its own merit, you can’t go cumulative and referee the last incident differently to how you refereed the other two incidents.”
Following the goal, Ballard was sent off for a second yellow and midfielder George Saville booked with both played now ruled out of Monday night’s game with Luxembourg through suspension.
On Ballard’s second yellow, O’Neill said: “The Slovakian dug-out that caused that as much as anything.”
“The [second] yellow card for Daniel is a joke,” the manager continued.
“If you look at it back, it is poor.”
“He is a top referee, he has refereed the Champions League final, he should have disallowed the goal.”
The victory, which keeps alive Slovakia’s hopes of qualifying automatically for next summer’s tournament, sparked huge celebrations from the hosts with O’Neill describing their reaction as “disappointing”.
“Everything was on the line for Slovakia. You could tell that by the way their technical area behaved towards the end of the game. Which was disappointing.
“Disappointing for their coach not to shake my hand.
“Ultimately, we congratulate Slovakia because they have a to go to Germany and win the group.”
