Equatorial Guinea had the first chance of the first half when Ivan Bolado had the ball nicked away from him just as he was about to shoot at the Libyan goal.
Equatorial Guinea had the ball in the net on 17 minutes when Aboud allowed Balboa's effort to squirm under him. However, the goal was ruled out for offside.
In a slow-moving second half, Lawrence Doe's powerful free kick was well-saved by Aboud as Libya struggled to create many chances.
Ahmed Zuway had a chance to make the breakthrough for the Libyans late on, but his effort flew wide after a goalmouth scramble.
Equatorial Guinea finally took the lead with two minutes to play as Balboa broke the offside trap before curling the ball past Aboud.
Libya nearly drew themselves level instantly, but Djamal Mahamat poked the ball inches wide from inside the area.
Balboa came close to grabbing his second of the match in the final minutes as his drive came back off the crossbar.