The Phobians midfielder Winful Cobbinah was able to recapture the scintillating form that has fuelled Hearts to recover from their poor start to the campaign, assisting the opener and scoring the match-winner.
Hearts coach Frank Elliott Nuttall made three changes to the starting XI that drew 3-3 with Bolga All Stars in Tamale, with Sam Yeboah, Kassenu Ghandi and Patrick Razak handed starting role.
The hosts had the better start of the game to unsettle Wafa, as Paul Acquah scored the opener on third minute when he headed in Cobbinah's cross from a free-kick.
Efforts from Majeed Ashimeru, Justice Amate and Caleb Amankwaah threatened Hearts' goal but were not enough to beat goalkeeper Samuel Akurugu.
Komla Agbegniadan pounced on an error from Vincent Atinga to equalise shortly after half-time, but his effort was saved by Akurugu and Patrick Razak fluffed another opportunity on the other side.
Cobbinah capped a wonderful day with a goal on 63rd minute when Wafa goalkeeper Razak Abalora failed to catch his curled free-kick with first attempt, bundling it into his own net.
The visitors brought on Richmond Lamptey to replace Aminu Musah, which changed their game plan, as they began to surge forward for a goal. Abdul-Wahab Ibrahim finally pulled one goal back through a header by the 88th minute.
Wafa threw men forward in search of the winner but Hearts were resolute at the back and held on for their sixth victory of the campaign, moving to third position with 23 points, six points behind Wafa who are also tied with Aduana Stars.
The Phobians will face Liberty Professionals in the Accra derby on Sunday at Carl Reindolf Park while Wafa host Inter Allies in Sogakope.