Two second half goals from Prince Obeng Ampem and Daniel Agbloe Lomotey were enough to silence Kotoko and widen the gap between them to 10 points.
Despite Wafa losing key midfielder Majeed Ashimeru and goalkeeper Razak Abalora, following their transfers to clubs outside the country, they still looked dangerous with Gideon Waja, Kennedy Boateng and Ampem in midfield while Lomotey and Togolese international Komla Agbegniadan led the attack.
The hosts threatened Kotoko in the third minute, after Agbegniadan was brought down outside the visitors' box but Waja saw the resulting kick going wide, before Kotoko's captain Amos Frimpong blocked Ampem's effort a minute later.
The Porcupines finally found their first real opportunity to draw first blood by the 19th minute, after Yakubu Mohammed combined with Emmanuel Gyamfi but the former's last ditched effort could not find the target.
After the break, Wafa stepped up the tempo and were rewarded with several opportunities but their forwards fluffed them. On the 51st minute, Ampem connected a pass from his teammate and lobbed his effort past onrushing goalkeeper Felix Annan, but the Wafa striker was flagged offside.
However the hosts took the lead seven minutes later through Ampem after Danso was brought down outside Kotoko's box.
Kotoko coach Steve Polack responded with a substitution, bringing on Frank Sarfo Gyamfi for Baba Mahama, and resorting to counterattack, but they still failed to find a breach in Wafa's defence.
Wafa made it 2-0 by the 68th minute through Lomotey and compounded Kotoko's miseries with the visitors failing to even complete two passes as a result of frustrations. And Although, they pushed men forward to at least get a consolation, their efforts were fruitless.
Wafa have now gone 41 league games unbeaten at home and have recorded their tenth straight home victories this season, the first of its kind in the club's history.
Kotoko will welcome Bolga All Stars to the Baba Yara Sports on Sunday while Wafa host title holders Wa All Stars once again.