Slovenia went through to next month's World Cup playoffs after winning 3-0 at San Marino.
The visitors ended up second in Group Three after Slovakia finished top thanks to a 1-0 win in Poland.
Milivoje Novakovic put Slovenia ahead midway through the first half and Dalibor Stevanovic doubled their advantage in the second period before Marko Suler added the gloss nine minutes from time.
Slovenia, who qualified for Euro 2000 and the 2002 World Cup, beat Slovakia 2-0 away on Saturday to move two points behind the leaders but their bid for automatic qualfication came too late.
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