Captain and centre-back Ammar Jemal slammed the ball past goalkeeper Felipe Ovono from close range with three minutes left in the first leg of the final to silence most of the 30,000 Soweto crowd.
Etoile host the return match at the 25,000-seat Stade Olympique in Mediterranean resort Sousse next Sunday and a goalless draw will bring the Confederation Cup back to the club after an eight-year absence.
A 1-1 draw at FAR Rabat of Morocco set the Tunisians up for their 2006 triumph with a stormy second leg ending 0-0 and Etoile succeeding on the away-goal rule.
Pirates are hoping to became the first South African winners of a CAF club competition since Kaizer Chiefs lifted the now defunct African Cup Winners Cup
14 years ago.
The Buccaneers have scored in all seven away matches en route to the final of the second-tier African competition and must do so again in Sousse to have a chance of overall success.
Pirates were lucky to be ahead at half-time after Iheb Msakni had a goal ruled offside and star Algeria-born striker Baghdad Bounedjah and Hamza Lahmar went close.
Bounedjah beat onrushing Ovono to the ball only for his shot to trickle wide while Lahmar forced a reflex save from the Equatoguinean goalkeeper.
Lahmar came even closer just past the hour as his free-kick flew over off the crossbar with Ovono beaten.
A cagey second half lacked the pace and goalmouth drama of the opening 45 minutes with Etoile largely content to contain Pirates.