Striker Vedat Muriqi scored an early penalty for the hosts in Pristina, with Zymer Bytyqi doubling the lead moments later.
Shayne Lavery headed home for the visitors on the stroke of half-time before Muriqi grabbed his second soon after the break.
A header seven minutes from time by Daniel Ballard, Northern Ireland’s best player on the night, produced a late flurry from the visitors, with Conor McMenamin failing to connect with a great chance to snatch an equaliser.
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