It brings to an end a three-match winless streak for the Lions of the North.
Meanwhile, Baroka have now won just one of their last nine matches and are in increasing danger of slipping in to the relegation zone.
The first decent opportunity of the game fell to Highlands Park. Mogaila Mokete whipped in a tantalising cross which Ryan Rae met on the volley but the effort was straight at Baroka goalkeeper Elvis Chipepeze, who looked as if he had gathered the ball behind his goalline, but it was not picked up by the match officials.
The home side began to stamp their authority on the match but it was the visitors who took the lead in the 16th minute against the run of play. Baroka midfielder Orebotse Mongae fired in a dipping free-kick which was met at the near post by captain Mduduzi Mdantsane, who produced an unstoppable glancing header in to the far corner which left Highlands Park goalkeeper Marlon Heugh with no chance.
The goal seemed to lift Bakgaga and they began taking the game to their opponents. Key to their dominance was the fact they were winning the midfield battle.
However, the hosts equalized on the stroke of the half-time. Ryan Rae's long throw was well flicked on by captain Bevan Fransman for Sello Motsepe to power home the header from close range as the sides went in to the interval locked at 1-1.
Both coaches would have been worried with the lack of goalscoring opportunities being created as both goals came from set-pieces. Abafana Bes'thende shook things up at the interval, replacing Danny Phiri with Lungelo Dube.
The second half saw the home side turning the tables and grabbing control of the game. Credit must go to Owen da Gama for whatever was said to his charges at half-time.
Rae's long throws were causing the Bakgaga defence plenty of problems and it was from one of these that Highlands Park almost profited a few minutes after the interval. In the 52nd minute, Mothobi Mvala gave the Lions of the North the lead grabbing his eighth goal of the season and moving in to second place on the Premiership top goalscorers' list when he expertly headed home from a delightful Sabelo Nyembe delivery.
Baroka almost equalized in the final minute of regular time but Heugh showed excellent reflexes to parry away Goodman Mosele's deflected volley and ensure his side came away with the three points on the day.
Highlands: 1 Heugh, 5 Fransman, 20 Ramoraka, 21 Mokoena, 34 Motsepe, 24 Rae, 14 Mvala, 40 Mahlangu, 31 Nyembe (Bunting 90+3’), 47 Ndoro (Mbatha 60’), 12 Mogaila (Haoseb 84’).
Subs: 30 Peters, 45 Haoseb, 43 Mbatha, 22 Williams, 13 Bunting, 33 Sibande, 3 Shongwe.
Baroka: 1 Chipezeze, 2 Kgoetyane, 21 Mongae (Makgaka 60’), 33 Sibiya, 20 Patjie, 14 Mosele, 39 Madigoe, 8 Mdantsane (Mabeba 67’), 36 Semenya, 42 Vilani (Dickens 55’), 3 Gebardt.
Subs: 30 Dlamini, 12 Makgaka, 43 Ntswane, 15 Chinyengetere, 28 Dickens, 25 Sodi, 13 Mabeba.