The result was the Moroccans’ second straight victory in the group while condemning Songo to another defeat as they languish at the foot of the group.
Arguably the best Africa-based player at the moment, El-Kaabi was on fire again with a second half double to add on to an assist he provided in the group's opening 1-0 win over Al-Hilal at home.
Now with six points and two clear at the top, Berkane will host second-placed Al-Masry in their next match.
El-Kaabi opened the scoring by turning in Abdessamad El-Mobaraky's attempt on 64 minutes, just five minutes after Songo were reduced to 10 men following a red card to midfielder Cremildo.
Togo international Fo-Doh Kodjo Laba provided for El-Kaabi’s second goal 11 minutes from time as Berkane managed to keep another clean sheet.
Songo have now conceded four goals without reply after they fell to a similar scoreline to Al-Masry on Matchday One.
In another match in Omdurman, Al-Masry bagged an away point in the 1-1 away draw with 10-man Al-Hilal.
Although they could have emerged with three points away from home, Al-Masry blew up their early lead and could not fully make full use of their numerical advantage by allowing Al-Hilal to force a draw with a late equaliser.
It was an evening of red cards in this group as Al-Hilal played 65 minutes of the match with a man down after El-Taher El-Hag Hassan was sent off for roughing up Farid Shawki but still managed to claim their first point of the campaign following a defeat to Berkane in their group opener.
It took just 10 minutes for Al-Masry to strike first through Islam Issa as they appeared to be on course for maximum points especially after the sending off of Hassan.
Brazilian striker Geovane Maranhao hit back for Al-Hilal from the penalty spot eight minutes from time after Burkinabe defender Mohamed Koffi had handled inside the box.
Despite gaining a point, Al-Hilal remain winless and on third place while Al-Masry surrendered top spot to settle on second with four points.