It wasn’t until the end of the first half that this Group F fixture exploded into life, with Mozambique racing to a late two-goal lead.
After a quiet first 30 minutes, the opener came from a well-worked set-piece routine, with Geny Catamo whipping a ball into the box for Faisal Bangal to nod home from close range.
The outsiders doubled their advantage moments later when Domingues was dragged down in the box by Gabon’s Bruno Ecuele Manga, with Catamo stepping up to convert from 12 yards.
Things were almost made even better for Mozambique when Witi rattled the crossbar, but instead of a 3-0 lead, they had to settle for a 2-1 advantage, as Pierre-Emerick Aubameyang was on hand for Gabon to reduce the arrears with the last kick of the half.
There was no drop in tempo after the break, as the scoring continued almost immediately after the restart.
After seeing their two-goal lead cut in half before the interval, Mozambique broke in behind the Gabon defence, with Witi picking out right-back Diogo Calila, who had ghosted into the box and managed to direct a downward header beyond Loyce Mbaba and restore their margin.
On the verge of creating history, the Mozambique nerves were intensified 14 minutes from time when Alex Moucketou-Moussounda tucked home a bouncing ball in the box to set up a grandstand finish.
Hernani Siluane had pulled off a stunning save, but the goalkeeper’s efforts were rendered meaningless, as the rebound fell to the feet of a grateful Moucketou-Moussounda.
Tension resonated through the Mozambique players in the closing stages, but at the 16th time of asking, they were victorious in an AFCON encounter.
Their qualification chances received a huge boost as a result, while Gabon sit bottom of Group F having lost both of their first two games.
Flashscore Man of the Match: Witi (Mozambique)