The Sudanese joined APR of Rwanda, which came from behind to beat Lydia Academic in the other group match.
Eid Abakar Mugadam set the ball rolling for Shendi after six minutes when he went past two defenders and fire home for the opener.
The Somali champions pulled one back through Mohamed Mahad Haji before Mugadam took the game beyond the Somalis with the third goal for Shendi.
Heegan captain Mohamed Ali Alkhidir Ali scored a contender for goal of the tournament on 86 minutes but it was little enough to earn them a point.
The win took Shendi to second place in the group with four points, five points behind leaders APR of Rwanda, which beat Lydia Academic of Burundi 3-1 in the group’s other match.
It was the neighbour’s from Burundi who badly wanted to win the game to seal their place in the last eight and they went up when Aziz Abdoul Nahimana accepted a gift from APR’s goalkeeper Claude Ndoli.
A cross from the right was met by Uwimana Messe who headed home but Ndoli's save was stationery and Nahimana gladly tapped it home on 55 minutes.
Academic couldn’t consolidate their lead and at the hour mark they gave away a penalty when Kiza Fataki handled in the vital area. Patrick Sibomana leveled matters from the spot.
The Burundians pushed for a winner but APR stiffened their backline and got the winner at the stroke of full time through Issa Bigirimana for their third win at the tournament.
Heegan (Somalia) 2-3 Ahly Shendi (Sudan)