Lincoln tweeted a picture of their players and match officials waiting on the pitch in Gibraltar before issuing a statement saying the preliminary-round qualifier had been cancelled.
"We can confirm that UEFA cancelled today's scheduled UEFA Europa League clash between ourselves and FC Prishtina," Lincoln said in the statement.
“The matter has now been referred to the UEFA Control, Ethics and Disciplinary Body for them to make a final decision on how the situation is resolved. The club waits patiently on their decision.”
The game was initially scheduled for last Tuesday but was postponed after eight Prishtina players tested positive for COVID-19 upon arrival in Gibraltar.
The match was due to go down as an automatic 3-0 win for Lincoln but Prishtina registered new players on loan from rival clubs under new UEFA rules for the rescheduled game.