The first leg of the final ended goalless in Rabat last weekend, leaving two-time winners Sfaxien firm favourites to win the second-tier African club competition.
Abdelfatteh Boukhriss put FUS, an unfashionable team promoted to the Moroccan first division only three seasons ago, ahead eight minutes into the opening half.
Hamdi Rouid levelled just before half-time and when veteran midfielder Kamel Zaiem converted a Tunisian penalty two minutes after the break an air of inevitability hung over the game.
But star-less FUS are nothing if not fighters and mid-year signing Mohamed Zouidi levelled on 74 minutes and snatched the match-winner one minute before full-time.
Boukhriss and Zouidi were unlikely stars for the Moroccans as they had not scored before in a competition won five years ago by another Rabat club, military outfit FAR.
A capacity 30,000 crowd left Taieb Mhiri Stadium in the Mediterranean city of Sfax on the east coast of Tunisia stunned after seeing the home team lose at home for the first time in the competition after 23 victories and a draw.
It was also the first time Sfaxien had conceded more than one goal at home in a Confederation Cup tie since making their debut three seasons ago against Guinean outfit Satellite.
Heightening the promise of a Tunisian success was a 3-0 home triumph for Sfaxien over FUS when they met at the group phase of the competition with experienced African campaigner Hamza Younes netting twice.
The result completed a disastrous end to the year for Tunisian clubs in Africa with Tunis-based Esperance humiliated 6-1 on aggregate by TP Mazembe from the Democratic Republic of Congo in the Champions League final.
FUS earned 660,000 dollars for emerging victorious after an 18-match campaign that began last February and included journeys to Tunisia (twice), Senegal, Guinea, Mali, South Africa, Egypt, Zambia and Libya.
And the Moroccans will get a chance to boost the club bank balance by a further 75,000 dollars at the end of January when they visit Lubumbashi and confront Mazembe in the annual, one-off African Super Cup match.