Rakhale chipped goalkeeper Rami Jridi from the edge of the area in the 47th minute to snare the spoils for the Buccaneers.
Pirates remain second in Group B with six points from three matches - three points behind Egyptian giants Zamalek, who defeated AC Leopards 2-0 in Cairo earlier in the day. Leopards and Sfaxien have a point apiece.
The Sea Robbers started brightly, as Lehlohonolo Majoro was foiled by Jridi in a one-on-one situation after being released by Myeni.
At the other end, Zied Derbeli tested Brighton Mhlongo with a low free-kick drilled through the wall, but the Bucs goalkeeper was alert and equal to the task.
Eric Tinkler's men should have been awarded a penalty just before the interval as Myeni was taken out by Wajdi Saidani in the box when approaching a Majoro cross. However, the referee was unmoved.
The visitors, though, stole ahead soon after the interval as Rakhale made a tackle before racing ahead and beating Jridi with a finish of the highest order.
Pirates managed to protect their lead thanks to some good work from Mhlongo in the latter stages, but lost the services of Thabo Matlaba in the 70th minute through injury, with fellow left-back Patrick Phungwayo taking his place.
Substitute Kermit Erasmus came close to extending the lead in the 85th minute but the nuggety forward was thwarted by an excellent stop by Jridi from close range.
Pirates XI: Mhlongo, Sangweni, Jele, Nyauza, Matlaba (Phungwayo 70'), Sarr, Manyisa, Rakhale, Myeni, Gabuza (Ntshumayelo 81'), Majoro (Erasmus 47').
Subs: Ovono, Masalesa, Makola, Memela.
Sfaxien: Jridi, Maaoul, Hannechi, Derbeli, Mereih, Ali Moncer, Saidani, Challouf, Louati, Ben Jemai, Mezlini.