Marco Silva's Estoril side, who reached the UEFA Europa League group stage with a 4-1 aggregate win over Austrian side Pasching in midweek, had won their opening two games of the season and climbed to third with the point on Monday.
Academica had lost their opening fixtures but took the lead with a fine goal in the 16th minute.
Brazilian midfielder Cleyton picked up a pass from Marinho on the right flank and cut into the box before cleverly turning past his marker and slotting underneath Vagner.
The hosts had won their previous five games in all competitions and pushed for an equaliser, but went in at the break frustrated and a goal behind.
However, they eventually made the breakthrough with 15 minutes to go.
Substitute Seba burst down the right wing, jinking into the box, only to see his low effort parried away by Ricardo, but Luis Leal was on hand to pounce on the rebound and turn home the equaliser.