Khaled Mouelhi converted a first-half penalty for the Blood and Gold at the Olympic Stadium in a Tunis suburb, but Farid Mellouli equalised for Chlef before half-time in a fiery Matchday 2 clash.
A shock appeared to be on the cards when Mohamed Messaoud put the Algerians ahead five minutes from time only for Mouelhi to convert another penalty, while Ndjeng scored his third goal of the competition to secure victory.
Esperance have six points from two outings after having beaten Sunshine Stars 2-0 in Nigeria two weeks ago, while Chlef are pointless after losing 1-0 at home to Tunisian outfit Etoile Sahel in the first series of group matches.
Etoile host Sunshine Stars in Mediterranean resort Sousse late on Saturday and success for the Red Brigade would strengthen expectations that the two Tunisian teams will advance to the semi-finals.
Both Group B matches are scheduled for Sunday with TP Mazembe from the Congo DR hosting Berekum Chelsea of Ghana and Zamalek confronting Al Ahly in an Egyptian derby.