Gervinho settled a tight game on the stroke of half-time as he ran unimpeded from the halfway line to curl home the match-winner from close range.
The Elephants had twice struck the post beforehand, with both Didier Drogba and Yaya Toure powering efforts against the woodwork.
Mali struggled against an Ivorian defence that has yet to concede a goal.
After Zambia had stunned Ghana when winning 1-0 in the day's first semi-final in the Equatoguinean city Bata, thoughts before the match had dwelled on the possibility of another shock result.
But Malian hopes of a surprise win over their West African rivals soon faced a reality check as the Elephants started the match in rampaging fashion.
Just six minutes in, captain Drogba headed a free-kick against the post from close range with Mali goalkeeper Soumaila Diakite beaten.
Ten minutes later, midfielder Toure hit the other post with even greater power as he ran onto Salomon Kalou's square pass before slamming against the upright with Diakite's goal lucky to emerge unscathed.
Bidding to reach the final for the first time since 1972, Mali's Eagles slowly clawed their way back into the match but only had a half-chance from Mustapha Yatabare to look back on for their first-half efforts.
Just as it seemed that Alain Giresse's side would go into the break with honours even, with Drogba and Kalou having wasted further openings, Gervinho finally made the breakthrough.
Picking up possession on the halfway line a fraction before Mali centre-back Ousmane Berthe, the Ivorian flew towards goal before opening his body to side-foot into the far corner from eight yards out.
That left Mali, who had lost their last three Nations Cup semi-finals, needing to find the first goal against the Elephants' defence at this tournament but they lacked urgency until the game's final quarter.
Kalou, who returned to the side after recovering from a thigh problem, saw Diakite tip over his curling effort before Yatabare finally registered a second-half effort at Boubacar Barry's goal - even if his volley flew over.
Shortly after, Drogba could have doubled the Ivorians' lead but Diakite deflected his angled strike to safety before Toure wasted a terrific opening when heading over a corner.
In a game littered by free-kicks, yellow cards and stoppages, Ivory Coast's orange-clad supporters finally started to believe as the minutes ticked by without Barry being forced into real action.
From the touchlines, coach Francois Zahoui looked on in the sternest fashion but a smile broke out once South African referee Daniel Bennett blew his final whistle four minutes into added time.
The Ivorian players revealed their own delight when kissing the turf in celebration and dancing a jig towards their fans as the Elephants reached the final for the first time since 2006 - and only their third overall.
On Sunday, the 1992 champions will take to the field in Libreville's Stade de l'Amitie again as this 'golden generation' tries to win only the country's second title against a Zambian side that has never won the trophy.
Meanwhile, Mali - who looked tired following their quarter-final exertions when beating Gabon on penalties on Sunday - must travel to the Equatoguinean city Bata to play Ghana in Saturday's third-place play-off.
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