In eye-catching scenes after the match - which Berkane won 3-0 to overturn a 2-0 first-leg deficit - visiting players, fans and officials appeared to vent their frustrations at the official, who appeared to be surrounded as bottles and other objects were thrown at him.
However, Ndiaye has denied reports that he was the figure in the video being hassled by Sfaxien's players.
"I was not beaten up," Ndiaye told Les Echos, as per Dakar Midi. "It should be noted that it is not me who appears in the video circulating on the internet and on social networks.
"Nobody attacked me, it's my second assistant who was assaulted."
First-half goals from forward Kodjo Fo-Doh Laba, Omar Nemssaoui and Issoufou Dayo sent the Moroccan outfit into the final, where they will square up with Egyptian giants SC Zamalek.
The first leg takes place on May 19 in Berkane, before the reverse match in Alexandria seven days later.