Ingwe finished the match one man less after Aziz Okaka was sent off for a second bookable offense.
Ugandan striker Davis Kasire came off the bench to score the only goal in the 79th minute, barely six minutes after replacing Harambee Stars forward Moses Shummah.
This is Homeboyz second title in the club’s history after winning FKF Cup last season.
Apart from the trophy, Homeboyz pocketed Sh1 million in prize money, while AFC received Sh500,000.
Mulembe United clinched the bronze medal after stunning Nzoia Sugar 2-1 in the third place playoffs.
The National Super League side walked home with Sh250,000 while Godfrey Oduor’s charges bagged Sh200,000.
Prime Cabinet Secretary Musalia Mudavadi gave an additional Sh100,000 to all the four participating clubs.
In the Mulembe – Nzoia match, Joseph Wafula broke the deadlock in the 27th minute for the millers but his celebration was cut short by Kevin Sagida’s equaliser just three minutes later.
Kendrick Onzore scored the winner in the 81st minute after capitalising on Nzoia’s defensive blunder.
By Francis Onguko