The Porcupine Warriors were undone by two penalties in Tarkwa, a result which played into the hands of the Academy Boys.
Wafa are the new leaders of the Ghana Premier League after matchday 10's round of games on Wednesday.
The Academy Boys handed 2014-15 champions Ashanti Gold a 3-0 defeat at Sogakope to propel themselves to the top of the ladder. Prince Ampem, Daniel Lomotey and Gideon Waja scored to ensure three points at the Red Bull Soccer Arena.
Asante Kotoko, leaders ahead of the matchday, could not hold on to Ahmed Adams' lead, as Paul Aidoo netted twice from the spot to give Medeama a 2-1 home win at the Tarkwa T&A Park. The Porcupine Warriors have consequently fallen to the third position.
Liberty Professionals conceded late as second-placed Aduana Stars stole a point at the Carl Reindorf Park. Bright Adjei scored in the 85th minute to cancel Samuel Sarfo's opener.
Hearts of Oak risked giving up a three-goal lead until Cosmos Dauda scored in the 84th minute to seal a 4-2 win over Bechem United at the Accra Sports Stadium. Thomas Abbey, Richard Akrofi and Fatawu Mohammed gave the Phobians a 3-0 first half lead before Nana Antwi Manu and Abdul Bashiru found the back of the net within nine minutes after recess for the visitors. The Phobians have moved to fifth on the standings.
At the El-Wak Stadium in Accra, Inter Allies' Isaac Osae and Stephen Sarfo of Berekum Chelsea traded goals as the two sides settled for a 1-1 draw.
In Cape Coast, current top scorer Nicholas Gyan fetched his seventh goal of the season as his Ebusua Dwarfs side were held to a 1-1 draw by Tema Youth. Joseph Paintsil was on target for the away team.
And finally in Tamale, Bolga All Stars claimed full points thanks to Emmanuel Anaba Permadu's 90th minute goal, which earned a 1-0 triumph over Elmina Sharks.
Great Olympics' game with Wa All Stars has been rescheduled due to the latter's delayed arrival from the Wafu tournament in Senegal.
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