The forward from South African club Orlando Pirates netted in each half after Ishmael Wadi had put Zimbabwe ahead in a lively Group B match in Bafoussam.
Mhango recently returned to action after a lengthy injury layoff and became only the third player after Cameroonians Vincent Aboubakar (twice) and Karl Toko Ekambi to bag a brace so far in this Cup of Nations.
Guinea and Senegal share the Group B lead with four points each after two rounds of matches, Malawi have three and Zimbabwe are pointless.
Group winners and runners-up qualify automatically for the round of 16, along with the best four third-placed teams.
On Tuesday, Malawi face 2019 runners-up Senegal in Bafoussam while Guinea meet Zimbabwe in the Cameroonian capital, Yaounde.
After the presence of Liverpool duo Sadio Mane and Naby Keita in the first half of a double-header - a 0-0 draw between Senegal and Guinea - there were no instantly recognisable Malawi or Zimbabwe stars.