Hamrun Spartans’ hopes of reaching the UEFA Conference League group stage for a second consecutive season were dashed in heartbreaking and highly controversial circumstances after a stoppage-time penalty handed Faroese champions NSÍ Runavík qualification.

The Maltese champions looked set to force extra time after battling back from a goal down in an evenly contested encounter, only for a contentious decision deep into added time to swing the tie in favour of the visitors.

NSÍ, who currently top the Faroese Premier League, made full use of their physical presence throughout the match, but Hamrun matched them in intensity and created enough chances to keep their European dream alive.

The Spartans made an encouraging start, with Damir Ceter twice threatening in the opening stages. The Colombian striker first directed a close-range header straight at the goalkeeper before another powerful effort was tipped behind for a corner.

The visitors gradually grew into the contest and broke the deadlock through Michal Przybylski, whose powerful strike from outside the area beat Célio at his far post.

Hamrun coach Stefano Sanderra responded decisively at the break, introducing Éder and Lucas Villela, and the changes transformed the home side’s attacking play.

The equaliser arrived early in the second half when Ante Ćorić produced a stunning volley from the edge of the area that flew into the net, sparking jubilant celebrations among the home supporters.

The goal lifted Hamrun, who pushed relentlessly for a winner. Villela went close after breaking into the penalty area, while Célio produced an excellent save to deny NSÍ from a dangerous free-kick.

Ćorić then narrowly missed the target with a long-range effort before Matthew Guillaumier fired over, as Hamrun continued to pile on the pressure.

With extra time appearing inevitable, the tie descended into controversy.

Deep into stoppage time, Tobias Hestad chased a loose ball towards the byline and managed to hook it back into the penalty area. Television replays appeared to show that the ball had already crossed the goal line before Hestad kept it in play, but neither Luxembourg referee Jeremy Muller nor his assistant signalled for a goal kick.

Believing the ball had gone out of play, Hamrun captain Emerson Marcelina picked it up inside the penalty area to place it for what he thought would be the restart.

Instead, the referee awarded NSÍ a penalty for deliberate handball.

Peter Knudsen calmly converted from the spot to seal qualification for the Faroese side, leaving Hamrun players and supporters in disbelief.

A devastated Marcelina was reduced to tears and requested to be substituted, leaving the pitch to a standing ovation from the home fans after an otherwise outstanding display.

The dramatic conclusion sparked angry scenes after the final whistle, with several Hamrun players confronting the match officials, while supporters voiced their frustration from the stands. The refereeing team eventually left the field under police escort.

For Hamrun, it was a cruel end to another spirited European campaign, with a controversial decision denying the Spartans the opportunity to continue their quest for another memorable run in continental football.