Seeking a first win of the season at the third attempt, Academica claimed a seventh-minute lead on home soil in somewhat unorthodox fashion.
A free-kick from Ricardo Nascimento struck the post before rebounding off the back of goalkeeper Lukas Raeder and over the line.
To their credit, Setubal responded strongly to equalise through Frederico Venancio inside 10 minutes.
Yet that proved to be the final goal of the game as both defences held firm thereafter.
Setubal now boast four points from three games, having defeated Gil Vicente 2-0 last weekend, while Academica's hunt for a maiden victory will continue at Boavista after the international break.
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