Both sides were desperate for a win after losing their opening matches of the tournament and it showed as they threw caution to the wind from the kick-off.
Chances were created at both ends of the pitch as defence took a back seat to attacking flair.
Despite having less possession and fewer shots on goal, Mozambique opened the scoring in the 37th minute when an unmarked Faisal Abdul Bangal got on the end of a Geny Catamo cross to head his side into the lead.
Ernan was sensational in the Mozambique goal, pulling off save after save to preserve his side's lead as Gabon pushed for an equaliser before Catamo was able to double their advantage from the penalty spot in the 42nd minute.
Gabon eventually managed to pull one back on the stroke of half-time deep into stoppage time at the end of the first half, when Pierre-Emerick Aubameyang reacted first to a rebound to poke the ball past Ernan.
However, it did not take long for Mozambique to restore their lead after the break, with Witi making a break down the left wing before lifting a cross onto the head of Diogo Calila, who made no mistake from close range to make it 3-1 in the 52nd minute.
Gabon continued to search for a way back into the match but were thwarted by the excellent Ernan time and again as he finished the match with eight saves.
They did find a consolation goal in the 76th minute when Alex Moucketou-Moussounda blasted home from close range after a goalmouth scramble around the Mozambique box.
Ultimately, Mozambique were able to hang on for their first-ever win at an Africa Cup of Nations tournament and keep their hopes of qualifying for the knockout rounds alive.
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Bafana Bafana midfielder Thalente Mbatha has insisted that South Africa remain in control of their Africa Cup of Nations destiny, despite suffering a narrow defeat to Egypt in their second group-stage encounter.
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