Both sides were left to settle for a share of the spoils following an eventful Primeira Liga clash that saw two penalties awarded and the visitors end the game with 10 men.
Setubal opened the scoring after 27 minutes as Brazilian forward Rafael Martins turned smartly on the edge of the area and sent a low finish into the bottom corner.
However, the hosts levelled just six minutes later, midfielder Marcos Paulo converting from the spot after Pedro Queiros handled Djavan Ferreira's attempted pass.
And the evening got worse for Setubal immediately afterwards as Martins was taken off on a stretcher with an apparently serious injury.
Yet five minutes before the break, the visitors were handed a chance to retake the lead from the penalty spot after Academica defender Joao Real was adjudged to have brought down Betinho just inside the area.
But attacker Ricardo Horta squandered a glorious chance to make it 2-1, sensationally scuffing a rebound onto the crossbar after Academica goalkeeper Ricardo had saved his penalty.
Ricardo Dani was also presented with a glaring opportunity from that resulting rebound, but he could only head over from point-blank range.
Setubal were then reduced to 10 men just before the hour mark when defender Adama Sene was ruled to have prevented a clear goalscoring opportunity with a foul on Marcos Paulo.
Still, despite their numerical advatange, the hosts could not find a winner, resulting in a draw that leaves Setubal four points adrift of the Europa League places in seventh, with Academica a point further back in ninth.
