Freese, who served as Johnson's assistant at Stars last term, collected three points thanks to a brace from Man of the Match Mogakolodi Ngele and strike from substitute Henrico Botes, with the latter making his 100th outing for the North West club.
The loss was United's heaviest of the season, resulting in Moroka Swallows overtaking them at the summit due to a healthier goal difference.
The Dube Birds and Matsatsantsa have 15 points - two more than fourth-placed Dikwena.
Vuyo Mere and Sameehg Doutie went close for their respective sides in the opening 10 minutes.
Stars captain Mere had a deflected free-kick go just wide of Rowen Williams' post while Doutie failed to convert from close range following a good run from former Dikwena winger Thuso Phala.
Williams was forced into a good save by Tintswalo Tshabalala in the 17th minute of the encounter. Tshabalala fired a fierce effort at goal but Williams was up to the task. Bevan Fransman also did well clearing the ball from danger with Mthembu ready to pounce on any scraps.
David Mathebula squandered a glorious chance to give the visitors the lead nine minutes later. Sibusiso Zuma, making his first appearance of the season, picked out an unmarked Mathebula in the area but the midfielder was unable to direct his header on target from point-black range.
Botes replaced the injured Siphelele Mthembu in the 28th minute and the newcomer made an early impact, scoring seven minutes later. The Namibia international controlled a long ball forward brilliantly before directing his effort past an out-of-position Williams The goal was Botes' 29th in the colours of Dikwena, extending his record as the club's all-time leading scorer.
Stars continued to press forward and nearly doubled their lead through Robert Ng’ambi a minute before the break. The Malawian lost his marker but was unable to get on the end of a Tshabalala’s corner-kick with an open net beckoning.
Dikwena went into the break, well deserved 1-0 leaders.
Ngele doubled the home side's lead five minutes into the second stanza. The Botswana international found himself in space before directing his effort past Williams and into the back of the net via the inside of the post.
Ngele got his second goal in the 65th minute. The Dikwena midfielder picked up the ball from Ng’ambi before making a darting run through the heart of SuperSport’s defence and sliding the ball into the back of the net.
The 23-year-old went close to bagging a hat-trick three minutes later but he was unable to beat Williams.
However, the home side comfortably saw out the encounter to end a two-game winless run and bounce back from a 2-0 defeat to Swallows.