A five-minute second-half brace from Walid Soliman completed a surprisingly comfortable victory over opponents who have upset several big clubs during their debut season.
Success was all the sweeter for record six-time African champions Ahly as they lacked three key players, with defender Ahmed Fathi, midfielder Mohamed Aboutrika and striker Emad Moteab on Olympic Games duty.
Each club finished with ten men at the Military Academy Stadium. Richard Boateng of Berekum was sent off just before half-time and Ahly veteran Wael Gomaa followed suit midway through the second half.
Ahly have nine points after previous victories over TP Mazembe from Democratic Republic of Congo and Cairo neighbours Zamalek, while Berekum exceeded expectations by defeating Zamalek and holding Mazembe.
The Cairo Red Devils, who last won the title four years ago, were quick out of the blocks and led within 17 minutes as Abdullah Al Saied connected with a clever back-pass to rifle the ball past goalkeeper Ernest Sowah.
A glancing Mohamed Naguib header from a corner doubled the Egyptian advantage before leading Champions League scorer Emmanuel Clottey raised his season haul to 12 by winning and converting a late first-half penalty.
But Soliman put the new kids on the block firmly in their place with a couple of superb left-foot goals approaching the closing stages to leave Berekum needing urgent defensive repairs before the sides' 19 August clash in Accra.
He controlled the ball with his chest on the edge of the box, turned and flicked it over an opponent before giving Sowah no chance, and soon after volleyed an awkward-height cross into the roof of the net.
Late show seals Mazembe win
In the other Group B match, the brilliance of Zamalek goalkeeper Abdel Wahed Al Sayed kept Mazembe at bay for 70 minutes before Ngandu Kasongo and Mbwana Samata scored the goals that brought a much-needed 2-0 victory.
Mazembe and Berekum have four points each and five-time Champions League winners Zamalek have yet to get off the mark at the halfway stage of the group, with the top two finishers advancing to the semi-finals.