Needing a win to keep the pace with rivals Porto, who thumped the struggling Beira-Mar 4-0 on Saturday, Benfica started slowly at Estadio EFAPEL.
Academica, who had drawn all three of their league matches to date, opened the scoring after 26 minutes when Guinea forward Salim Cisse converted a penalty given away by Benfica's Maximiliano Pereira.
The visitors responded with a spot-kick of their own, with Academica's Rodrigo Galo given a straight red card five minutes into the second half as a result.
Oscar Cardozo converted the penalty to level proceedings before amazingly, another penalty was awarded.
This time it was for Academica and Wilson Eduardo scored it, restoring the hosts lead.
Benfica boss Jorge Jesus introduced Brazilian attacker Lima in a bid to snare a late equaliser and the move paid off, as he netted the equaliser five minutes from time.
Both sides remain unbeaten in the competition this season.
In other matches, Sporting Braga moved to third with a 4-1 success against a 10-man Rio Ave.
Forward Eder bagged a brace in the win, while Ruben Amorim and Custodio also netted for Jose Peseiro's side.
Vitor and Cicero scored in the last five minutes for Pacos de Ferreira as they came from behind to claim a 3-3 draw at Nacional.
In the thrilling match - which saw both sides reduced to 10 men - Pacos kept their unbeaten run alive with their late heroics.
Vitoria Setubal's win over Olhanense was a more sedate affair, with Cameroon Albert Meyong's second-half penalty enough for them to secure a 1-0 triumph.