A vibrant Orlando Stadium dominated by Orlando Pirates fans was silenced in the 58th minute when Tresor Tshibwabwa Yamba Yamba headed in a Keleto Makgalwa corner kick to put Sekhukhune into the lead.
The goal highlighted the Buccaneers' struggle to defend set-pieces, something that cost them in the Caf Champions League.
To cap a difficult outing for the Soweto giants, defender Nkosinathi Sibisi was shown a red card with five minutes to go.
Wednesday's 1-0 defeat gave an advantage to log leaders Mamelodi Sundowns, who now enjoy a 12-point lead ahead of second-placed Sundowns.
The result saw third-placed Sekhukhune close in on Pirates to two points, although the Buccaneers have played four matches fewer.