Galaxy made four changes, as they recalled Ebrahim Seedat, Luckyboy Mokoena, Bathusi Aubaas and Mokete Mogaila while Sekhukhune brought back Talent Chawapiwa, Seun Ledwaba and Tlotlo Leepile.
The Rockets were fired up in the early stages, putting Babina Noko under pressure but they were let down by their finishing.
Mxolisi Macuphu had a glorious chance to break the deadlock for Shaun Bartlett's charges on the half-hour mark after going through on goal but he dragged his shot wide.
The hosts kept on creating chances in the closing phase of the first stanza but the lack of a killer-instinct gave Sekhukhune a reprieve, as the first stanza ended goalless.
Galaxy continued where they left off early in the second stanza and Macuphu was unlucky not to break the deadlock for the hosts just before the hour-mark with a header that came off the frame of goal after a cross by Lindokuhle Mbatha.
Babina Noko were playing on counter-attacks and MacDonald Makhubedu needed fresh legs upfront in the 63rd minute as Prince Nxumalo replaced Chibuike Ohizu while two minutes later Tshegofatso Nyama came on for Mogaila in a tactical change by Bartlett.
Ethan Broos had a glorious chance to get the breakthrough for Galaxy in the last 20 minutes after going clear on goal but he blasted his strike over the bar.
The Rockets were caught on a quick counter-attack in the last ten minutes, as Pogiso Mahlangu was clinical for the visitors, firing a strike into the roof of the net, 0-1.
Brooks had another good chance to level matters for Galaxy in the last six minutes but his strike inside the box was saved by Toaster Nsabata and Sekhukhune held on to their second win of the season.
Galaxy: Van Der Linde, Sanoka, Makitan, Seedat, Mokoena, Mbunjana, Brooks, Aubaas, Mbatha, Macuphu, Magaila.
Subs: Kolak, Nduli, Mahlangu, Lekay, Bodibe, Phohlongo, Nyama, Ndwandwe, Mngomezulu.
Sekuhkhune: Nsabata, Mobbie, Chawapihwa, Motsepe, Gyimah,Leepile, Maart, Madonsela, Ledwaba, Jampies, Ohizu.
Subs: Kapini, Rakhale, Matona, Patjie, Mahlangu, Parusnath, Nxumalo, Sibanyoni, Shai.