Substitute Dean Ebbe scored within two minutes of coming off the bench to send The New Saints into the Champions League second qualifying round.
Kosova’s Feronikeli scored two late goals to secure a draw in the first leg at Park Hall, leaving the Welsh champions needing to score in Pristina.
Chances were few in a nervy first half at the Stadium Fadil Vokrri.
Ebbe replaced Adrian Cieslewicz on 65 minutes and made an instant impact to head in Simon Spender’s cross.
Saints can now look forward to facing Danish champions FC Copenhagen in the second qualifying round, with the first leg to be played on 23 or 24 July.
Feronikeli drop into the Europa League, where they will come up against either Slovan Bratislava of Slovakia or Montenegro side Sutjeska.
New Saints manager Scott Ruscoe told BBC Sport Wales:
“It was definitely exciting towards the end. Although we didn’t create lots and lots of chances, the one that mattered Dean Ebbe certainly put it away well.
“I did look at the clock and thought ‘ah no, it’s going to happen again (conceding a late equaliser)’ but not tonight, the lads were resolute, willing each other on despite a few tired legs out there.
“Copenhagen will be tough, a top European side, played in Champions League group stages, lots of experience and they play good football.”
