Pirates' win moves them back to within three points of Mamelodi Sundowns in the table, with a game in hand on the Tshwane giants.
Jose Riveiro's side battled to break down a well-organised Magesi, even after the Limpopo side had Leglogonolo Mokone sent off in the 39th minute.
Mofokeng produced a moment of magic to secure the Buccaneers a ninth win in 10 Premiership games. But it might have been different had Magesi's Wonderboy Makhubu scored a penalty in first-half stoppage time.
In the 4th minute, midfielder Makhelene Makhaula tried his luck from long-range, but Elvis Chipezeze made a fine save.
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