With 15 minutes played, Kotoko earned a huge chance to take the lead with a penalty but Songe Yacouba failed to hit the back of the net with his effort.
Regardless, they continued to push for the opener with Dwarfs hitting back with occasional counter-attacks.
With barely 10 minutes to end proceedings at the virtually empty Baba Yara Stadium, Coach Maxwell Konadu’s decision to introduce Mathew Cudjoe and Richard Arthur paid off as two goals in a space of three minutes condemned Dwarfs to their fifth loss after five games.
16-year-old Mathew Cudjoe scored the game’s opener in the 83rd minute before Richard Arthur put the game to bed with Kotoko’s second after the 86th minute.
The win is the red’s third of the campaign and lie 6th on the league table.