The 22-year-old scored the first goal after seven minutes and created the second in the final minute for Alaa Marzouki as the Tunisian club won the quarter-final 3-2 on aggregate.
In the semi-finals, Sfaxien will meet Renaissance Berkane of Morocco, who crushed hapless Gor Mahia of Kenya 5-1 in the second leg to complete a 7-1 overall triumph.
Nine-time CAF title winners Zamalek of Egypt moved closer to lifting an African trophy for the first time since 2003 when they edged Hassania Agadir of Morocco 1-0 in Suez.
It was the only goal of the two legs and secured the White Knights a semi-final showdown with Etoile Sahel of Tunisia or Al Hilal of Sudan.
Etoile take a 3-1 lead into a second leg postponed until April 22 over security concerns following the midweek ouster by the military of veteran Sudanese autocrat Omar al-Bashir.
Chaouat was a 10-year-old schoolboy when Sfaxien first won the Confederation Cup, the African equivalent of the UEFA Europa League, in 2007.
He soared above several Nkana defenders to nod a corner past goalkeeper Kelvin Mulenga into the corner and give Sfaxien a perfect start.
Tanzanian Hassan Kessy wasted a chance to equalise when his timid shot went wide as goalkeeper Aymen Dahmen darted off his line.
Chaouat was denied a second goal when his header off another corner was brilliantly pushed away by Mulenga.
A Ronald Kampamba header three minutes from time rebounded off the woodwork to rob Nkana of an equaliser and soon after Sfaxien delivered the killer blow.
Chaouat threaded a perfectly weighted pass past several defenders and Marzouki sprinted clear to score from close range.
Meanwhile, Berkane equalled the record overall winning margin for a Confederation Cup quarter-final as they toyed with Gor and should have won more decisively.
Kodjo Fo-Doh Laba put Renaissance ahead after 21 minutes with his sixth goal of the competition, making the Togolese one of the three leading scorers this season.
Lawrence Juma levelled almost immediately after sloppy defending, but Berkane took control to lead 3-1 at half-time thanks to goals from captain Mohammed Aziz and Badr el Helali.
Burkina Faso defender Issoufou Dayo notched the fourth goal and the romp was completed four minutes from time when unmarked substitute Youssef Essaiydy poked the ball into the net.
In Suez, Ibrahim Hassan was the match-winner for Zamalek, scoring on 49 minutes in a tense affair as Hassania vainly sought an away goal after the first leg ended 0-0.
Success for the five-time African champions eased some of the disappointment felt by Egyptian supporters after the exit of Al Ahly from the CAF Champions League.
Ahly, winners of an unrivalled 19 CAF titles, defeated Mamelodi Sundowns of South Africa 1-0 in the second leg of a quarter-final, but bowed out 5-1 on aggregate.