Boateng clinched three points in the 82nd minute after running onto a brilliant pass from Obed Owusu and shooting past goalkeeper Danso Wiredu Mensah.
Owusu gave Kotoko the lead after 15 minutes but a resilient Dwarfs side equalized through Solomon Okudzeto eight minutes into the second half.
Buoyed by the goal, Dwarfs went all out for maximum points but were dealt a huge blow as Awudu Masawudu was sent off for a second bookable offence.
Thereafter the game tilted in favour of the hosts who grabbed the winning goal with eight minutes remaining.
The win means Kotoko have not lost a home game since their 0-1 loss to New Edubiase on 23rd April 2016.
They occupy the fourth position and are three points behind leaders AshantiGold while Dwarfs have dropped to the relegation zone.
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