It was fourth time lucky for the Malian Eagles as they lost three previous third-place matches in the African football showpiece, while the Black Stars were suffering a second loss in three play-off appearances.
Striker Asamoah Gyan, who missed a penalty in the semi-final loss to Zambia, was a notable omission as Ghana made four changes with suspensions ruling out defender John Boye and midfielder Derek Boateng.
Mali also had four new faces compared to the side that took Côte d'Ivoire to the wire in the other semi-final with goalkeeper Oumar Sissoko, defenders Ousmane Coulibaly and Abdoulaye Maiga and striker Garra Dembele coming in.
Ghana dominated the cagey early exchanges at a sparsely populated Nuevo Estadio de Malabo in the only to fall behind midway through the opening half.
A clever corner routine saw the kick from Barcelona midfielder Seydou Keita find Bakaye Traore just outside the box and when Adam Kwarasey failed to grasp his low drive, Diabate reacted quickest to poke the ball over the line.
There could have been a second goal for the Eagles ten minutes later as a swift counter exposed the Black Stars defence, but when Kwarasey failed to hold a low Samba Diakate shot there was no Malian to take advantage this time.
With Ghana seldom threatening the Malian defence, coach Goran Stevanovic introduced striker Prince Tagoe for midfielder Samuel Inkoom nine minutes before half-time. Another substitution by the four-time champions and four-time runners-up saw experienced Sulley Muntari introduced for the second half in place of fellow midfielder Mohammed Abu.
Muntari thought he had levelled early on in the second half when he fired past Sissoko from close range, but the effort was ruled out for offside. Ghana suffered another blow as the slow-tempo match entered the final quarter when defender Vorsah was given his marching orders after a second caution.
The fate of the Black Stars was sealed in the closing stages as overlapping full-back Adam Tamboura crossed and Diabate timed his run perfectly to tap the ball past Kwarasey.