Florent Ibenge’s side became the first team to win two African Nations Championship titles, having won the inaugural CHAN tournament in 2009.
Elia Meschak scored twice for the well-experienced Congolese side, in the 29th and 62nd minute, while Jonathan Bolingi added the third in the 73rd minute to subdue the Malians who came with the intention of winning their first title.
DR Congo’s clean sheet on the night made it the second time they lifted the CHAN trophy without conceding a goal in the final.
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Earlier in the day, Ivory Coast clinched third place following a 2-1 win over Guinea.