The Indomitable Lions made wholesale changes to the side that lost on penalties against Egypt in the semi-finals, as only goalkeeper Andre Onana and Samuel Gouet were retained, with the likes of Vincent Aboubakar and Karl Toko Ekambi benched.
The Stallions settled the quicker of the two sides, as Abdoul Tapsoba forced a save out of Onana in the 11th minute with a low strike towards the bottom corner.
Steeve Yago eventually broke the deadlock for Kamou Malo's charges in the 24th minute with a looping strike in the box after a cross by Issa Kabore.
Burkina Faso continued to put Cameroon under pressure and they went 2-0 up just before the half-time break after Onana spilled Kabore's cross at the near post into his own net.
Toni Conceicao made a double attacking change at half-time, as he brought on Aboubakar in place of Gouet and Nicolas Ngamaleu replaced Ignatius Ganago.
However, Djibril Ouattara made it 3-0 for the Stallions four minutes into the second stanza with a header past Onana after a cross by Bertrand Traore.
Cameroon started to gain attacking momentum after they also introduced Toko Ekambi and Stephane Bahoken eventually pulled a goal back 18 minutes before time with a close-range strike from a rebound in the box.
The Indomitable Lions were fired up after that, creating more chances and Aboubakar pulled a second goal five minutes before time with a header from a corner.
Aboubakar completed the comeback for Cameroon two minutes before time with a strike in the box from a corner to complete his brace, and ultimately sending the game to penalties.
The Indomitable Lions went on to triumph 5-3 in the shoot-out, with Ambroise Oyongo netting the winner after Onana saved Blati Toure's spot-kick.