Esteban Becker's men knew only a win at Estadio de Bata on Sunday would be enough to secure their progression from Group A, and Balboa's spot-kick put them in front before a late second goal from Iban Salvador ensured they advanced to the last eight of the tournament for only the second time.
Gabon will feel hard done by with the opening goal, as referee Noumandiez Doue harshly adjudged Lloyd Palun to have upended Balboa.
Equatorial Guinea will not care about that, though, after securing their first win of the competition to qualify as runners-up behind Congo.
