Substitute Amr Gamal, who came off the bench on the hour in place of veteran Emad Meteb, scored the winner after 75 minutes at the Suez Military Stadium.
Haythem Jouini gave Esperance a 25th-minute lead at Stade Olympique which they held until 60 seconds from time when Baghdad Bounedjah equalised.
The Algerian struck again three minutes into stoppage time to earn 2006 Confederation Cup winners Etoile maximum points and condemn Esperance to a fifth loss in six group games.
Zamalek, the great Egyptian and African rivals of Ahly, lead Group B going into a top-of-the-table Cairo clash on Sunday with fellow qualifiers Orlando Pirates of South Africa.
Pirates have the same number of points as Zamalek, but trail on head-to-head records having lost 2-1 when the former African champions met in South Africa two months ago.
Should Zamalek retain top spot they will face Etoile in the semi-finals with Pirates meeting Ahly in a repeat of the 2013 CAF Champions League final won 3-1 on aggregate by the Cairo Red Devils.
12.09.2015 19H30 Etoile du Sahel (Tunisia) 2-1 Esperance (Tunisia)
12.09.2015 20H30 Al Ahly (Egypt) 1-0 Stade Malien (Mali)
13.09.2015 15H30 AC Leopards (Congo) vs CS Sfaxien (Tunisia)
13.09.2015 20H30 Zamalek (Egypt) vs Orlando Pirates (South Africa)
*All times are in local time