Headers from Amr Gamal and Gedo in the second half ensured the Egyptian Premier League leaders triumphed, while in the other Confederation Cup fixture, Real Bamako had to come from behind for a 1-1 draw at home to ASEC.
Due to previous clashes between Ahly fans and Egyptian police, no supporters were allowed into the Petro Sport Stadium in Kattameya for the continental clash.
Nkana returned to Cairo for the first time since their 5-0 thrashing at the hands of Zamalek in March, which saw the Zambian Premier League champions dumped out of the CAF Champions League in the second round and drop into the Confederation Cup play-off round.
The visitors, who had not lost in all competitions since playing Zamalek, produced the best goal-scoring opportunity of the first half but Simon Bwalya shot just wide after pouncing on a defensive mistake by Ahly.
After a somewhat subdued first half, Ahly needed just one minute in the second to take the lead with Gamal flicking on Ahmed Fathy's cross just after the break.
Gamal almost doubled the home team's advantage soon after but his shot went over the bar, though Ahly did not have to wait long for a second goal.
In the 56th minute, a corner found Gedo at the near post and the striker headed powerfully past Rabson Mucheleng'anga in Nkana's goal.
The win took Ahly to three points at the top of Group B in the Confederation Cup, while the other two teams in the pool Etoile Sahel and Sewe Sport are set to play on Sunday.
Ahly have won a record 18 African titles but have never won the Confederation Cup.
In Group A, Ivory Coast's ASEC took the lead just after the hour mark away to Real Bamako through Michel Mvondo, but the home side hit back four minutes from time in Mali, with Moussa Kone scoring the equaliser.
With the other Group A match between Leopards de Dolisie and Cotonsport having been postponed, the draw was enough for ASEC to take top spot in the standings.
