The 31-year-old from the Democratic Republic of Congo struck on 75 minutes in the annual clash between the holders of the CAF Champions League and the second-tier CAF Confederation Cup.
The goal came after Imad Riahi was dispossessed by Mohamed Chibi as he tried to take the ball into the Pyramids' half at the 30 June Stadium in the Egyptian capital.
Moroccan Chibi pushed the ball into the Berkane area, and Mayele fired a low shot across goalkeeper Munir Mohamedi and into the net off the far post.
Mayele, who joined Pyramids in 2023 from Tanzanian club Young Africans, changed his first name from Fiston to Mahmoud after converting to Islam last month.
He was a key figure when Pyramids lifted the Champions League at only the second attempt last season, finishing as the leading scorer with nine goals in the premier African club competition.
Pyramids, whose victory was worth $500,000, are the third Egyptian club to win the Super Cup after Al Ahly (eight titles) and Zamalek (five).
Berkane were victorious in a previous Super Cup appearance three seasons ago.