Two stunning strikes from Adama Traore saw Mali take the lead after Ibrahima Wadji had opened the scoring for Senegal midway through the second half.
Senegal had an opportunity to level the match with five minutes to play, but Malick Niang's penalty was saved.
Diadie Samassekou clinched the match with a stoppage-time goal for Mali.
The frenetic final 25 minutes were a contrast to the opening half, when opportunities were rare and fouls were frequent between the west African neighbors.
There were 44 fouls in the match, but it developed into an enthralling encounter that saw two penalties saved and two spectacular goals.
Mali had the better of the early exchanges, but it was Senegal, making its first appearance in the under-20 tournament, which had the best opportunity in the opening half. Sidy Sarr fired a header that forced Djigui Diarra to leap to his left and make a superb save.
Moussa Ba was sent off for Senegal with a minute left in the first half for his second bookable offense. It should have buoyed Mali, but instead it was Senegal who benefited and Ibrahima, also known as Ibou, Wadji opened the scoring in the 64th minute.
Mali equalized in the 74th minute with arguably the best goal of the tournament as Traore's free-kick from outside the box curled into the top right corner to leave Senegal goalkeeper Ibrahima Sy stunned.
Moments later Mali had a chance to take the lead after a penalty was given, but Sy saved the weak effort from Falaye Sacko.
Mali soon made up for that miss when Traore, a Lille midfielder, added another highlight-reel goal as he eased past four defenders to drill his shot home and score his second goal in nine minutes.
Niang had a chance to equalize but his penalty was saved by Diarra with five minutes to play.
Mali then had the last say, with a brilliantly executed move that saw Samassekou dribble the ball past Sy.
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