The Cameroonian referee halted a match between hosts Ismaily and Tunisian opponents Club Africain in stoppage time after sections of the crowd hurled bottles on the pitch.
There had been a number of crowd-related stoppages at the Ismailia Stadium before the premature end to the Group C clash of former champions in which Africain were leading 2-1.
Egypt were chosen this month as replacement Cup of Nations hosts after original choice Cameroon fell behind with preparations and there were also security concerns.
While Egyptian football has a history of crowd disturbances, they usually involve one of the two most popular clubs, Al Ahly and Zamalek, who are both based in Cairo.
Ismaily, who lost their first group match last weekend, took an early lead when Namibian Benson Shilongo converted a low cross.
But Ghazi Ayadi converted two penalties late in the opening half to turn the game in favour of Club Africain, also matchday 1 losers.
The second spot-kick infuriated the crowd as the referee initially awarded a free-kick before altering his decision after consulting with an assistant.
Ismaily supporters became increasingly angry as the second half progressed and an assistant referee had to abandon his position with five minutes left after objects were flung at him.
With pleas for calm from the coaching staff of the Egyptian club being ignored, the referee called the match off in additional time.
CS Constantine from Algeria host leaders TP Mazembe from the Democratic Republic of Congo Saturday in the other Group C fixture.
A Karim Walid goal on 85 minutes earned record eight-time African champions Al Ahly a 1-1 draw away to group newcomers JS Saoura of Algeria in Bechar.
Sid Ali Yahia-Cherif had put the local club ahead just before the hour in the western city near the border with Morocco.
Ahly top Group D with four points, but could be overtaken by Simba SC Saturday if the Tanzanian outfit avoid defeat away to V Club from DR Congo.
Taha Yassine Khenissi bagged a brace as defending champions Esperance from Tunisia overcame limited FC Platinum from Zimbabwe 2-0 in Group B in an empty Tunis stadium.
The crowd ban followed trouble during both the semi-finals and final last year, including the stoning of the bus carrying Ahly to the stadium for the second leg of the title decider.
Khenissi, a shock nomination for the 2018 African Player of the Year award having failed to score a single CAF goal last year, netted after 24 and 56 minutes.
Orlando Pirates from South Africa lead Esperance on goal difference after a surprisingly comfortable 3-0 victory over Horoya from Guinea in Soweto.
Horoya, who held SuperSport United and Mamelodi Sundowns in African group matches near Pretoria during the past two years, were unlucky to only draw with Esperance last weekend.
But the form that enabled them to dominate the trophy-holders was not evident and Zambian Justin Shonga netted twice in the second half after Thembinkosi Lorch opened the scoring.
A further four matchday 2 fixtures are scheduled for Saturday with the clash of the 2016 and 2017 champions, Sundowns and Wydad Casablanca from Morocco, near Pretoria the highlight.