Jan Kozak's men missed the opportunity to grace the world stage in Brazil after finishing third in UEFA Group G behind Bosnia-Herzegovina and Greece.
However, since then Slovakia have bounced back well with victories over Poland and Israel, and they continued that winning trend in Senec.
Former Manchester City midfielder Vladimir Weiss opened the scoring for Slovakia, missing a 45th-minute penalty but keeping his composure to score the rebound.
It took until the 85th minute for the game to be put beyond doubt when Erik Jendrisek duly put his name on the scoresheet.
Montenegro - who themselves missed out on a place in Brazil - were also looking for a third consecutive triumph following wins over Luxembourg and Ghana, but were unable to find a way past a stubborn Slovakia outfit.
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