Togo's first win since 2019 saw them move 2nd of their CHAN 2020 group. It's also their first victory in the competition.
Tchatakora opened the scoring for Togo at the Stade de la Réunification before Kyeyune drew level three minutes later. Nane got the winner for the Sparrowhawks in the 57th minute.
In the earlier match on Friday, Morocco were held to a 0-0 draw against Rwanda.
The 2018 winners and highest ranked side had to settle for a point against the side 98 positions below them in the FIFA rankings.
Rwanda face Uganda on the final matchday while Morocco play Togo.