Gervinho's solo moment of brilliance deep into the first half gave the Elephants' a 1-0 win and left them on a collision course with Zambia, shock winners over Ghana in the day's other semi-final.
The pair meet back at Libreville's L'Amitie stadium on Sunday.
For the Ivorians this will be their first appearance in the Nations Cup climax since they were beaten by Egypt in Cairo in 2006.
They are seeking their second continental title after a lone success 20 years ago.
Mali had struggled manfully to keep the orange tide at bay in a frenetic first half, until Gervinho made his mark with a little help from some slack defending.
Depriving Mali back Ousmane Berthe of the ball bang on the halfway line the Gunners star scampered hare-like down the left wing, leaving Malian pursuers in his wake to shoot right-footed past Soumaila Diakite and into the far corner.
The Eagles coach Alain Giresse pounded the dug out with his fist in frustration.
The Ivorians went into this semi-final looking to avoid the same fate as Ghana, the Black Stars having been knocked out by so-called minnows Zambia across the border in Bata earlier.
The hot favourites switched three from Saturday's last eight win over Equatorial Guinea - Salomon Kalou, Cheik Tiote and PSG's Siaka Tiene in for Arthur Boka, Kafoumba Coulibaly and Max Gradel.
Mali made two changes from the side that won Sunday's stamina-sapping quarter-final against Gabon, with French-based forwards Cheick Tidiane Diabate and Moustapha Yattabare on for injured duo Abdou Traore and Modibo Maiga.
With Pele among the crowd at the three-quarters full 40,000-seater stadium Didier Drogba almost put the Elephants into a fifth minute lead when hitting the cross bar.
Berthe was booked seconds later and keeper Diakite had to look sharp to punch away the resulting freekick taken by the Ivorian skipper.
Ivory Coast could have been two up inside the opening quarter of an hour but Yaya Toure followed his captain's lead by also hitting a bar, the right post this time, after being set up by Salomon Kalou.
Down at the other end Ivorian midfielder Jean-Jacques Gosso had his work cut out to stop Diabate's charge in the box.
Drogba was then off target when he dragged his angled shot from the right after getting the better of his Mali markers Berthe and Drissa Diakite when he ran on to a long ball into the area.
In the last minute before the break Gervinho struck to put his team into a deserved lead.
Mali came out for the second half with an unenviable task - to become the first team at the tournament to score against Drogba and company.
But only Diakite's fingernails prevented them falling further behind around the hour when the Mali keeper diverted Kalou's shoot over the crossbar.
Yatabare had Mali's best chance in the 72nd minute, his attempt from the right narrowly going over Boubacar Barry's bar.
But the Ivorians held firm to march on while Mali made an honourable exit.
(For more sports news and updates, follow Ahram Online Sports on Twitter:@AO_Sports)
Short link: