Aubameyang put Unai Emery’s side ahead after converting his effort from the penalty spot in the ninth minute.
The penalty stretched his tally to 20 goals in 35 league outings for the Emirates Stadium outfit this season.
Glenn Murray’s leveller from the spot in the 61st minute earned a point for Chris Hughton's men in North London.
Alex Iwobi was later introduced for Granit Xhaka in the 77th minute but his contribution was not enough to seal maximum points for the hosts.
Leon Balogun was an unused substitute for Brighton and he continues his wait for a Premier League appearance since December 26 [vs. Arsenal] while Mali's Yves Bissouma was in action for the full 90 minutes.
Arsenal are fifth in the league table after gathering 67 points from 37 matches, three points adrift of the top-four and an inferior goal difference to fourth-placed Tottenham Hotspur.
They have been paired against Burundi, Guinea and Madagascar in Group B while Bissouma's Mali have been drawn in Group E against Angola, Mauritania and Tunisia.