The opening half saw the African side take the initiative, with Amadou Haidara going close from distance first from open play and then from a set-piece, but Croatian stopper Adrian Semper equal to both efforts.
Koita showed Haidara how to finish clinically. Sidiki Maiga expertly hooked a long crossfield ball back behind him as he sprinted towards the Croatian touchline. The 15-year-old forward followed up and hit a low shot left-footed into the bottom right-hand corner across Semper.
Mali held firm, and will head to La Serena for a final four showdown against either Belgium or Costa Rica, who face off in Concepcion tomorrow.