Neither side could progress any further in the tournament after managing just one win between them before Thursday night's game, with Plzen and Atletico Madrid already certain of advancing from Group B.
The hosts had previously taken only a solitary point from their five games, but gave a 12,000 crowd something to cheer on Thursday night with goals from substitutes Victor Mare (57) and Hanan Maman (80).
Academica still finished third in the group on five points, although manager Pedro Emanuel saw his side fail to continue their proud record of having scored in every game.
Chances were hard to come by in the early stages with Santos Nivaldo trying his luck from distance for the visitors on 11 minutes, only to fire wide.
Hapoel took some time to get into their stride before creating their first serious chance on 29 minutes.
Salim Toama's left-footed free-kick was tipped over the bar by Academica goalkeeper Romuald Peiser and from the resulting corner from the same player, Peiser was forced to punch clear to avert the danger.
Academica missed a good chance to go in front on 37 minutes when Arnaldo Edinho headed wide from 12 yards out, while Tomas Marinho fired over from a similar distance with the first effort of the second period.
The deadlock was finally broken in the 57th minute when Mare, who had only been on the pitch for 10 minutes, turned the ball home from six yards following a cross from Gil Vermouth.
And it was another substitute who sealed the win after 80 minutes.
Maman had also only been on the pitch for around 10 minutes when he got on the end of Mare's header back across goal to head home from 12 yards.