NORTHERN IRELAND have only one chance remaining of making it to the World Cup finals after this setback at a stunned Windsor Park.
They go to the Czech Republic, knowing a victory in their final qualifier will be needed next month if a place in the play-offs is to become possible.
Goals from Stanislav Sestak and substitute Filip Holosko either side of half-time saw Slovakia cement their place at the top of Group Three.
Northern Ireland slipped down to third in the table on goal difference behind Slovenia and it was a disappointing performance, given the way they had picked up a point against Poland at the weekend.
It was also the first home defeat suffered in seven competitive games by Northern Ireland and as such unexpected.
Yet they could have gone ahead inside 60 seconds. David Healy tested goalkeeper Jan Mucha after Martin Paterson played the ball back to him.
Northern Ireland, though, were rocked back on their heels after 15 minutes two minutes later when Slovakia made the breakthrough. Manchester City winger Vladimir Weiss, son of the manager of the same name, skipped past Evans and slipped it to Sestak, who made no mistake.
Northern Ireland almost hit back in the 27th minute when Grant McCann picked out Healy but he sent his effort wide of the post.
Then the North struck a good spell and Slovakia were suddenly looking a bit vulnerable at the back.
Johnson then found space down the right in the 63rd minute but his cross only found goalkeeper Mucha.
Paterson again came close two minutes later after being picked out by Healy on the left but Mucha reacted superbly to beat away his shot.
Slovakia made it 2-0 in the 66th minute following a swift counter-attack with substitute Holosko knocking the ball past Maik Taylor two minutes after stepping off the bench.
N IRELAND: Taylor, McAuley, Craigan, Hughes, Evans, Johnson, McCann (McGinn 70), Clingan (Baird 70), Davis, Paterson (Brunt 76), Healy.
SLOVAKIA: Mucha, Strba, Pekarik, Skrtel, Zabavnik, Durica, Weiss (Sapara 90), Kopunek, Sestak (Holosko 65), Stoch (Jendrisek), Vittek.
Referee: Bjorn Kuipers (Holland).
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