Northern Ireland defender Chris Baird slammed Russian ref Nikolay Ivanov for refusing to award a "blatant" penalty.
Ivanov waved away appeals after Baird's goalbound shot appeared to strike a raised hand inside the Slovakia area.
And the Slovaks made it 2-0 less than a minute later.
Baird said: "It was a definite penalty. I said to him 'it's a penalty'. He said 'I know, it hit his hand'. I said 'why didn't you give it then?' "But he was having none of it. He knows it hit the hand yet he didn't give it."
Second-half goals from Martin Skrtel and Marek Hamsik killed off Nigel Worthington's team before Jan Durica handed the visitors a late lifeline by diverting Chris Brunt's cross into his own net.
"We didn't play well and to concede from two set-pieces was terrible," added Baird.
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