Michael Yeboah’s second-half effort condemned the 23-time champions to their first defeat of the season in the outstanding matchday three fixture.
The result has dropped the Porcupine Warriors a place down on the league table from ninth to 10th, while the opposition takes a giant leap from 14th to 5th.
In their first of four matches in the coming 10 days, Kotoko coach Maxwell Konadu made two changes to their starting line-up, bringing on Abdul Latif Anabila and William Opoku Mensah.
New Brazilian signing Fabio Gama Dos Santos was once again not named in the matchday squad.
In the end, Yeboah emerged hero of the day as he headed home Abdul Manaf’s cross in the 54th minute to decide the fixture.
The defeat was not Kotoko’s only worry from the fixture. Former Atalanta left-back, on his second appearance for his new club after a recent transfer, was substituted 10 minutes to half-time after picking up an injury.
The full-backs situation is a major headache for the Porcupine Warriors as they are set to take on Dreams FC on Sunday and Sudanese side Al-Hilal in the Caf Champions League next week.
The game was played in Accra as the Kumasi-based fold are having to take time away from the traditional Baba Yara Sports Stadium due to ongoing renovation works.
So far this season, Kotoko have won one (a 1-0 win over Legon Cites) of four Premier League games, drawing two (1-1 with Eleven Wonders on matchday one and 1-1 against Berekum Chelsea) and losing one.
The club has set their sights on winning the top-flight for a record 24th time and their first since beating Heart of Lions to the title in 2014.
Olympics, on the other hand have won their second game of the season, their first three points coming courtesy of a 3-0 home triumph over Legon Cities. Their performance statistics include one draw (1-1 against Medeama) and one defeat (2-0 loss to Liberty Professionals).