Starting for the first time at the tournament following injury, Borussia Dortmund striker Haller connected with a Max-Alain Gradel cross in the 65th minute at the Ebimpe Olympic Stadium, his shot looping over the goalkeeper and in.
That was enough to settle a tense but open semi-final showdown, and the Ivorians will now face Nigeria at the same venue on Sunday to decide who takes the title.
The two-time champions are the first host country to reach the final of the Cup of Nations since Egypt in 2006, and the turnaround is absolutely remarkable for a team that was on the brink of elimination in the group stage.
In contrast, it was an agonising defeat for DR Congo, who had been dreaming of a first appearance in an AFCON final since they were champions as Zaire in 1974.
Ivory Coast's run at the tournament had been described on the eve of this game as "miraculous" by their own interim coach Emerse Fae, the man who replaced the sacked Jean-Louis Gasset following embarrassing results in the group stage.
Humiliated and on the verge of elimination after a 4-0 defeat by Equatorial Guinea on January 22, this was their first match at the Ebimpe Olympic Stadium on Abidjan's dusty outskirts since then.
The Elephants scraped through to the last 16 as the last of the four best third-placed teams, then ousted reigning champions Senegal on penalties. They followed that by beating Mali in the quarter-finals - despite playing most of the match with 10 men - with their winner coming in added time in extra time.
Oumar Diakite, the match-winner against Mali, was sent off while celebrating his goal and was suspended here along with captain Serge Aurier, Odilon Kossounou and Christian Kouame.
Among those coming in were Brighton winger Simon Adingra, who got the equaliser against Mali, and Haller, the talismanic forward who was finally fully fit. DR Congo were looking to avenge their 3-1 defeat by the Ivorians in their last appearance in the AFCON semi-finals, in 2015.
Congo protest
Their players have been spurred on during this tournament by a determination to raise awareness of the plight of millions of Congolese affected by ongoing violence in the east of the country.
The Congo team used the national anthem to protest, each covering their mouth with one hand and using the other to imitate a gun pointing at their heads. Apparently unperturbed by the hostile home crowd, the Leopards started well and had the ball in the net in the ninth minute.
Cedric Bakambu knocked the ball out of goalkeeper Yahia Fofana's grasp and in at a corner, but the goal was disallowed by the Libyan referee for a foul. The biggest chances of the first half fell to the Ivorians, who grew as a threat as the interval approached.
Haller rose unmarked in the box only to somehow head wide from Wilfried Singo's inviting cross in the 40th minute. Moments later, Franck Kessie crashed a shot off the post. Kessie threatened again just before the hour mark with a powerful strike that forced goalkeeper Lionel Mpasi into action, but the breakthrough followed soon after.
Max-Alain Gradel held up a cross into the box from the right and Haller swung his leg in hope rather than expectation. The connection was not great but the ball bounced down into the ground and then looped over the head of the helpless Mpasi and into the net.
Frenzied celebrations ensued, while Fae leapt around in his technical area. The hosts then went for the kill, with Haller heading onto the roof of the net from an Adingra corner and sending a lob wide when left with just Mpasi to beat. One goal was enough and a deafening roar greeted the final whistle.