A heavy downpour nearly saw referee Badir Yasin call off the game at half-time after declaring the pitch waterlogged but 40 minutes later, action resumed after consultations between both teams and match officials.
Wafula scored his two goals inside the opening ten minutes, opening the scoring after four before striking again five later.
An own goal from Harambee defender James Situma halved the deficit on the hour mark before substitute Edwin Ombasa equalised for Stanley Okumbi’s charges in the 73rd but veteran Charles Okwemba had the last word four minutes to full time.
The first half belonged to Ingwe who were determined to end their three game winless run this season against Mathare as Bernard Mang’oli, Okwemba and Humphrey Mieno dominated the midfield.
Mathare resumed a more rejuvenated side but keeper Patrick Matasi did well to stop Harrison Mwendwa and Daniel Mwaura long range shots to see Ingwe start their title defence on a winning note.
Leopards will now meet Ligi Ndogo in the pre-quarter finals.
In the Kenyan Premier League, hosts Chemelil Sugar and Western Stima played to a goalless draw while relegation threatened Nairobi City Stars failed to collect maximum points away to Bandari after the match ended to a barren stalemate.
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