Mthokozisi Msomi netted a last-gasp winner soon after Katlego Mtwaisha cancelled out Asive Langwe's first-half opener at Bidvest Stadium.
Wits dominated the match early on with experienced players Erwin Isaacs and Langwe in the thick of things. Pirates, who were undefeated in their first two matches, come close to conceding a goal 16 minutes in when Msomi’s shot from inside the box flew inches wide of the goal post.
On 20th minutes, Pirates striker Sibusiso Mahlangu got the first real chance of the match when he went one-on-one with Tumelo Taunyane but the Wits keeper stood tall and palmed the shot wide for a corner kick.
Wits took control of proceedings midway through the first half, as Isaacs initiated a counter-attack before releasing a perfect pass into the path of Teboho Moerane. The Wits wing galloped up the field before putting in a telling cross for Langwe to open the score with a great diving header.
In the second half, Wits picked up from where they left off as Mupondo Masuko’s well-taken shot from long-range shaved the upright and went over the bar. But Pirates came close to equalising in the 62nd minute when skilful player Neo Marks played a great cross for Seanago Maslwaelo, who shot inches wide from inside the penalty box.
In the last few minutes, the tempo of the match went up as Pirates went in search of an equaliser. The Buccaneers were rewarded for their persistence when substitute Mtwaisha scored with a great volley after Khumbulani Mkhize headed a Masuku corner his way.
However, Wits responded a minute later when Isaacs crossed for Msomi, who turned his marker before unleashing a powerful shot past a helpless Philani Zikalala.
Bucs thought they had drawn level in optional time but Mahlangu's effort was correctly disallowed for a hand-ball.
Wits (4-4-2): Tumelo Taunyane – Sandile Motladile, Renanao Leepile, Marckus Lecki, Tebogo Moerane – Siya Mose, Mupondo Masuko, Erwin Isaacs, Asive Langwe – Mthokozisi Msomi, Tshidiso Monamodi (Elasto Kapowezha 76th)
Coach: Charles Yohane.
Pirates (4-4-2): Philani Zikalala – Khumbulani Mkhize, Lehlohonolo Mtshali, Khanya Gwala, Tercions Malepe (Mthokozisi Sithole 31st) – Sibusiso Faku (Siyanda Ngubo 46th), Siphesihle Sangweni, Neo Marks, Seanego Maslwaelo (Katlego Mtwaisha 61st) – Menzi Masuku, Sibusiso Mahlangu.
Coach: Augusto Palacios.