Samassa was unlucky not to score his second goal of the game three minutes before the half-time interval, as he saw his shot clip the post and go out of play.
Ghana were given a lifeline to launch a comeback into the match when they were awarded a penalty 10 minutes later.
Coulibaly was controversially adjudged to have handled the ball inside the Mali area, but Wakaso failed to convert the resulting spot kick.
Keita thought that he had scored his second goal on 72 minutes but it was ruled out for offside.
Ghana halved the deficit with eight minutes left on the clock, Diakite failing to read Kwadwo Asamoah's attempt from 25 yards and allowing it to sail past him into the net.
However, the Black Stars failed to score a late equaliser and Mali wrapped up the win in injury time with Sigamary Diarra's volley.