Two goals in a six-minute spell after halftime by Arber Zeneli and Atdhe Nuhiu earned Kosovo the points in the League D Group 3 match, which was also the first time they had staged a competitive game in Kosovo itself.
Dutch-based Zeneli curled a superb shot into the bottom corner in the 50th minute and Nuhiu, who plays for English second tier side Sheffield Wednesday, doubled their advantage with a deflected effort to spark jubilant scenes at a packed Fadil Vokrr stadium.
Kosovo were admitted as members of UEFA and subsequently FIFA in 2016 following a long campaign during which they faced fierce opposition from Serbia.
They drew one and lost nine of their matches in the 2018 World Cup qualifiers and were held 0-0 by Azerbaijan in their opening Nations League match on Friday.
