Omer Damari's stoppage-time equaliser for Hapoel Tel-Aviv ended Academica's dreams of their first European win in more than 40 years in their 1-1 draw.
Salim Cisse looked to have earned the Portuguese side their first win in European competition since their 2-0 victory over FC Magdeburg in 1969 when he scored from close range just after the break.
However, Damari ruined the celebrations when he levelled the scores in the last action of the game with a header from the middle of the area as the Israeli side snatched a draw in their 100th match in UEFA competition.
Both teams had several chances and Academica goalkeeper Nunes Ricardo dealt with his first real test of the evening early on when he blocked Toto Tamuz's close-range shot with his feet, before defender Reiner Ferreira saw his strike at the other end blocked by Walid Badir.
Tamuz tested Ricardo again but the Portuguese keeper punched clear, with Bruno China clearing the resulting corner taken by Gil Vermouth.
Joao Dias then forced a save from Hapoel keeper Edel Apoula as the first half drew to a close with neither side able to break the deadlock.
However, things changed soon after the interval when Cisse put the home side in front almost immediately with a close-range strike.
The forward anticipated Tomas Marinho's ball from the right wing and slid the ball home from the middle of the penalty area.
Academia very nearly went 2-0 up five minutes later when Ricardo's long ball found Cleyton, whose drilled header hit the bar.
The hosts were in the ascendancy and were unlucky to not extend their lead when Wilson Eduardo's drilled header was punched clear by Apoula, before Marinho's 20-yard strike hit the post.
However, it was Hapoel who scored, with Damari's header deep into injury time snatching a draw for his side.