Junior Zindoga scored the only goal of the game in the 18th minute at the Seisa Ramabodu Stadium.
Usuthu appeared to have equalised in the second half but he goal wasn't given as the ball was adjudged to have not crossed the line.
Vilakazi's side then had a penalty appeal waved away after Rowan Human was upended inside the box.
Speaking after the game, the coach said on SuperSport: "Firstly, I'm very disappointed with the referee today.
"Everything was going against us, but we are very proud of Arthur [Zwane] for the effort of the players. They were working very hard, it was just not meant to be, but the effort was there."
Vilakazi added: "You can check maybe their goal, maybe that was not our best structures defensively and that's why we suffered, but other than that, they worked very hard and created chances which needed to be converted.
"I'm very much disappointed in the referees and their decisions apart from the goal, we are not a team that always complains about referees but this game was very bad and we suffered. That's disappointing for our football in South Africa."
Orlando Pirates clinched the Carling Knockout Cup in dramatic fashion at the New Peter Mokaba Stadium, edging Marumo Gallants 1-0 after extra time to secure their second trophy of the season.
Marumo Gallants' goalkeeper Washington Arubi says his side is comfortable being labelled the underdogs ahead of Saturday's Carling Knockout final against Orlando Pirates.
Orlando Pirates face Marumo Gallants in the Carling Knockout Cup final at Peter Mokaba Stadium on Saturday as they attempt to win their second trophy this season.
Orlando Pirates captain Nkosinathi Sibisi is keeping his focus sharply on the Carling Knockout Cup title as his team tops the Betway Premiership table with 28 points after 12 games.
