As the two teams struggled for a breakthrough, Magesi went one man down when Lehlogonolo Mokone was red-carded six minutes before half-time for a late tackle on Mohau Nkota.
Then right on 45 minutes, Relebohile Mofokeng was sent in a curler from just outside the box to thrust Pirates ahead for his second league goal of the season.
It wasn't Magesi's day amid some drama in the first half's stoppage time when Makhehlene Makhaula handled inside the box but Wonderboy Makhubu missed the resultant penalty kick despite sending Sipho Chaine the wrong way.
Having to make up for their numerical disadvantage, Magesi managed to limit the damage with some spirited defending in the second half as the Soweto giants went home with a slender 1-0 victory.
It was a result that saw second-placed Pirates restore the gap between them and log leaders Mamelodi Sundowns to three points going into the New Year, but the former have a game in hand.