Two goals from 18-year-old Ibrahim Moro and another effort from former Kotoko youth product Baakoh were enough to hand the visitors their second defeat in a row despite a consolation from Songne Yacouba.
Kotoko made three changes to the squad that lost the Super Clash last weekend to Hearts of Oak, with Sadick Adams making his debut league appearance this season, while Emmanuel Owusu replaced suspended Wahab Adams and Jordan Opoku returning from injury layoff.
The host, however, didn't make any change to the squad that lost to Bechem at Fosu Gyeabour Park.
By the 11th minute, Sougne Yacouba saw his pass to Frederick Boateng blocked while Sadick fired wide a minute later.
Karela claimed the lead by the 22nd minute through Imoro Ibrahim, who connected a long pass before firing past goalkeeper Felix Annan.
Sadick and Frederick Boateng pushed for the equaliser but their efforts failed to yield until few moments later when Yacouba pulled level for Kotoko.
Deep in first half, Karela were awarded a penalty which sparked protest from the Porcupines, who threatened to abandon the game, but the call stood and Moro successfully transformed to hand the hosts the lead once more.
By the 54th minute, goalkeeper Nii Kaala saved an effort from Sadick following a nice build up play by Kotoko.
After sucking the visitors’ pressure, Karela made it 3-1 through Baakoh, to add insult to injury.
Kotoko brought on Mawuli Osei and Akwasi Nti for Sadick and Yacouba respectively in a bid to reduce the deficit but all efforts proved futile.
Karela, who also defeated Hearts 3-1 on matchday eight, have moved two places up to third on the log with 17 points, three points behind leaders Ashanti Gold while Kotoko dropped to 10th with 14 points.