The loss in the penultimate fixture in the campaign does still damage their hopes of making it to North America, however, as they will enter those play-offs in the lowest group of seeds.
Slovakia originally thought they 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 goalkeeper.
Just eight minutes later, they had another strike disallowed by VAR after David Strelec was penalised for handling the ball when finishing from another Haraslin set-piece.
O’Neill felt that the decisions to rule out 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 on its own merit, you can’t go cumulative and referee the last incident differently to how you refereed the other two incidents.”
Following the winning goal, Ballard was sent off for a second yellow card offence and midfielder George Saville was booked with both players 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,” he 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 can go to Germany and try to win the group.”
