The match was played at the Stade Augustin Monedan Stadium in the capital Libreville.
A brace by USA-based striker, Jermaine Seoposenwe and a goal by Sanah Mollo saw the Sasol-sponsored Banyana Banyana return home with a positive result from the first leg.
The home side put the visitors under pressure in the opening minutes of the match, forcing them to concede a penalty as early as the third minute.
Banyana Banyana had a chance to level the score in the 15th minute, but a header inside the box was easily dealt with by the Gabonese keeper.
Seoposenwe equalised in the 25th minute. She beat the off-side trap before hitting the back of the net.
The South African ladies picked up momentum before the half hour mark with Seoposenwe coming close to extending the lead in the 25th minute, but her header landed in the hands of the keeper.
The striker made up for her earlier miss when she put Banyana Banyana in the lead in the 35th minute – tapping in after the keeper parried Refiloe Jane’s shot.
The visitors led 2-1 at the break.
Mamelodi Sundowns striker, Rhoda Mulaudzi registered her first cap when she came on for Amanda Dlamini at the start of the second half.
Gabon got back on level terms in 71st minute following another defensive error – after the visitors failed to clear from a set-piece.
But the South Africans restored their lead three minutes later with a Mollo goal.
Both teams pushed for more goals in the dying minutes of the game, but Banyana Banyana held on for an important 3-2 victory.
The win sees South Africa go into the return leg with an advantage of three away goals.
The return leg will be played at Dobsonville stadium in Soweto on Sunday, 31 May 2015.
Kick-off is set for 15h00.
Banyana Banyana are expected back in the country on Sunday morning (24 May).