Northern Ireland manager Nigel Worthington accused his side of believing their own publicity after Slovakia's victory seriously damaged their World Cup hopes.
Goals from Stanislav Sestak and substitute Filip Holosko either side of half-time saw the leaders cement their place at the top of Group Three.
With Slovenia beating Poland, Northern Ireland slipped to third in the table after their first defeat at home in seven competitive games under Worthington. It means the province will need to beat the Czech Republic in their final qualifier in Prague next month if they are to have any hope at all of making the play-offs.
After a shaky start by the home side, in the 15th minute Slovakia winger Vladimir Weiss, son of the manager of the same name, skipped past Jonny Evans on the right and laid the ball into the path of Sestak, who made no mistake from close range.
Northern Ireland rallied after the break but the game was put beyond them in the 66th minute following a swift counter-attack with substitute Holosko knocking the ball past goalkeeper Maik Taylor two minutes after stepping off the bench.
Worthington's side went into the match buoyant after their 1-1 draw in Poland on Saturday and he said: "Nice things had been written and nice things said. You start believing you do not have to work as hard as you should. That's garbage. We got our rewards – nothing.
"It is a mental thing when things are said by a lot of people and it is in their faces all the time, they take it on board," he added. "You try and get their feet on the ground to make sure things are right. We never started while they were bright and breezy. I feel gutted. If we had played for 90 minutes instead of 45 we would have taken something from the game. You are not going to win an international match with a 45-minute performance."
Martin Paterson and substitute Niall McGinn both came close in the second half but they could not break Slovakia's resistance. Without the aerial threat of the injured Rangers striker Kyle Lafferty, Northern Ireland were short of options up front.
But Worthington was in no mood to make excuses. He said: "We haven't got Lafferty, this, that and the other but you have still got to go out and perform. We turned up in the second half and looked like a side. At 1-0 you have a chance of getting back into the game, then they extended their lead.
"It was a disappointment the way we played because we had worked so hard to get to where we were. I said it yesterday, we were so close yet so far. We are now far away through an inept performance."
Northern Ireland (4-4-2): Taylor (Birmingham City); McAuley (Ipswich), Hughes (Fulham), Evans (Manchester United), Craigan (Motherwell); Johnson (Birmingham City), McCann (Scunthorpe), Clingan (Coventry), Davis (Rangers); Paterson (Burnley), Healy (Sunderland). Substitutes: Tuffey (gk), McGivern, Baird, McGinn, Ward, Brunt, Kee.
Slovakia (4-4-2): Mucha; Strba, Pekarik, Skrtel, Zabavnik; Durica, Weiss, Kopunek, Sestak; Stoch, Vittek. Substitutes: Kamenar, Cech, Holosko, Jendrisek, Pecalka, Salata, Sapara.
Referee: B Kuipers (Netherlands).