Senegal went into the encounter as strong favourites to beat Amajita given their success in the previous editions.
The Young Lions of Teranga played the last two Afcon finals, and while they failed to win any of them, they will fancy their chances this time around.
Coach Thabo Senong didn't tamper too much with the squad that has been representing the country so well in Niger, with Khulekani Kubheka keeping his place and the captain's armband on the night.
Kobamelo Kodisang started on the right-hand side while James Monyane led the attack alongside Promise Mkhuma.
Senong, however, left Nkosingiphile Ngcobo on the bench despite the Kaizer Chiefs' player's impressive performances at the tournament.
Senegal started brightly as they won their first corner of the game inside the opening 60 seconds following a clearance from Givemore Khuphe.
The South Africans should consider themselves fortunate not have conceded in the 12th minute as Faly Ndaw failed to beat Kubheka from Souleymane Aw's cross.
At this stage, it was clear that Amajita needed to defend better, and they did just that to frustrate the Senegalese team, who enjoyed the majority of the ball possession in the opening stages of the first half.
The game turned into a physical affair midway through the first period, but Senegal still managed to test Kubheka who dived to his right to deny Aw following an attempt from outside the box.
While they found themselves under immense pressure from Senegal, Amajita still threatened to score, and Luke Le Roux's long-range shot missed the target in the closing stages of the first half.
Both teams went into the dressing rooms locked at 0-0, and Senong would have been pleased with his team's defensive work.
Senegal continued to put Amajita against the ropes after the restart and in the 52nd minute, Ibrahima Dramé saw his attempt blocked before Kubheka came to the rescue with a fine save two minutes later.
Ousseynou Niang and Youssouph Mamadou Badji combined well inside the Amajita box on the hour-mark, but again Kubheka stood between Senegal and the opening goal.
Senegal didn't stop trying and they were duly rewarded when Khuphe put the ball past his own goal from an attempted shot inside the box in the final 20 minutes.
Amajita tried to recover from the setback, but Siphesihle Mkhize was denied right at the death as Senegal held on for their third successive Afcon final.
South Africa will now take on Nigeria in a 3rd/4th play-off match on Sunday.