Mahlonoka scooped the accolade with a fine strike against Black Africa Hopsol at the 2018 Future Champs tournament, as reported on the club's official website.
Fellow development player Zakhele Lepasa was also nominated for the prize.
Zambian hitman Justin Shonga won the gong in February with a stunning long-range finish against Chippa United.
Past recipients include experienced utility man Thabo Matlaba and youngster Ricardo Lourenco.
Fans voted for the winner on Pirates' social media platforms.