Gabon, who started their campaign with a 1-0 win over Cameroon, top Group D with four points from two matches, with Tunisia in second place on two points.
Alain Giresse's side will play their final group match against Zambia on Thursday while Tunisia will face Cameroon.
"I was really pleased with my team's performance in difficult conditions with this rain, it was difficult to control the ball," Giresse told a press conference.
"It was a good perfomance from my team. What we need to do is get a win in the final game," said Tunisia assistant coach Sami Trabelsi.
The Gabon Panthers dominated throughout but failed to convert a handful of chances through Pierre-Emerick Aubameyang and Stephane Nguema.
After a shaky start, Gabon took control of the game and came close to opening the scoring when Eric Mouloungui's diving header shaved Aymen Mathlouthi's post.
Tunisia hit back five minutes later as midfielder Amine Chermiti collected a through ball, only for Didier Ovono to dive at his feet in the box.
Aubameyang then broke down the right flank and unleashed a powerful drive that was parried away by Mathlouthi as the Panthers piled on the pressure.
Just before the break, Mouloungui again got the better of a hesitant Tunisia defence but his header went just wide.
The Carthage Eagles stepped up a gear after the interval but they failed to take advantage of an Ovono blunder as the clock ticked past the hour.
The scare spurred Gabon back into the game and Mathlouthi was made to work by a sudden Nguema floating drive from the right.
As the rain started to pelt down in Lubango, Gabon were denied a last-minute penalty when Ammar Jemel brought Daniel Cousin down in the area.
