Tendai Ndoro dropped to the bench, but Mothobi Mvala returned and Abdi Banda made his first start. Wits welcomed back Brandon Peterson with Lehlohonolo Nonyane in for Zitha Macheke.
The bright start to the match came from the Clever Boys after goalkeeper Marlon Heugh was forced to parry a dangerously taking free-kick from Deon Hotto after 18 minutes played.
The home side enjoyed large parts of possession following the half-hour mark, but that territorial advantage didn't transmit to the front-pairing who fired blanks habitually.
That particular scenario changed four minutes to halftime when Peter Shalulile fired home from the penalty spot following a foul inside the penalty area.
Buoyed by the opener, Highlands started the second half on a high whilst the Clever Boys restructured to conjure up a reply with the introduction of Mxolisi Machupu.
Momentum though remained firmly on the path of the home side who had the visitors under their spell from the wing and right through the middle of the park. Highlands adopted more firepower twenty minutes before full-time as Ndoro entered the equation for Ramagalela.
The Clever Boys leaned closer to the equaliser in the final minutes and were rewarded when Thabang Monare fired from the penalty spot right at the death.
The result does little to both sides positions on the table as either of the duo remain in fifth and sixth place respectively.
Highlands: Heugh, Mokoena, Mbhele, Banda, Rae, Mahlangu, Williams, Mbatha, Shalulile, Mvala, Ramagalela.
Subs: Peters, Mogaila, Msane, Letsholonyane, Fransman, Motsepe, Ndoro.
Wits: Petersen, Hlatshwayo, Nonyane, Monare, Domingo, Hotto, Hlanti, Mkhwanazi, Alexander, Motupa, Dzvukamanja
Subs: Goss, Pelembe, Nange, Macheke, Khunyedi, Ritchie, Macuphu