Gervinho flicked the ball past defender Ousmane Berthe with a deft back-heel and sprinted 30 metres into the penalty area to score just before half-time.
It was a magical goal that brought to life a toughly-contested game in which both tired-looking teams battled to find any rhythm.
"It was my pace that allowed me to get away. It was thrilling to score such an important goal," Arsenal's Gervinho told reporters.
The Ivorians will meet Zambia in Sunday's final in Libreville.
Zambia beat Ghana 1-0 in an upset in the other semi-final earlier on Wednesday in Bata, Equatorial Guinea, which is co-hosting the tournament with Gabon.
Ivory Coast proved too powerful for their fellow West Africans and might have won by a bigger margin.
"We were in a tough game and a little nervous at first but the experience of my players shone through and they managed all the key situations," said Ivory Coast coach Francois Zahoui.
Didier Drogba hit the crossbar early on with a header and a thunderous shot from Yaya Toure in the 16th minute also rattled the woodwork.
Mali were restricted to long-range shots with their midfield talisman Seydou Keita proving largely ineffective.
"We played a little bit of a static game and we must say hats off to Mali. But we are delighted to be back in the final," added Drogba who missed a penalty in the shootout when the Ivorians lost the 2006 final to hosts Egypt in Cairo.
Sunday's match will be third final for the Ivory Coast, who won the tournament in 1992.
Zambia will also play their third final having previously lost in 1974 and 1994.
