Highlands took an early lead through Rudi Isaacs, who reacted quickest after the home side failed to clear a corner, burying his shot into the roof of the net.
The Lions of the North almost made it 2-0 shortly afterwards – Jose Garcia’s cross-cum-shot beating Tapuwa Kapini in goals, but not the upright.
However, the hosts gradually found their footing and twice came close to equalising.
Just past the half-hour mark Siyethemba Mnguni won possession in the area before firing inches over.
They were even closer on 40 minutes – Bongani Ndlovu with a beautiful curling effort from the edge of the area which narrowly missed the target.
Highlands made their dominance count in the second half with another goal in the 64th minute, this time Mothobi Mvala heading in a set-piece delivery from the right.
And Mvala added a third goal and got his brace in the 75th minute, reacting quickest at the far post to nod in a half-cleared corner-kick from the left.
The result gives Allan Freese's side the early advantage in the three-team playoffs with an away-win already on the board. University of Pretoria host Mbombela in the next fixture on Sunday afternoon.
Mbombela: Xaba, Shongwe, Mabuza, Myango, Maphosa, Khumalo (Gumede 85'), Mnguni (Sekome 67'), Maliba, Mabde, Thomo (Nkosi 65'), Ndhlovu
Highlands: Kapini, Leonard, Isaacs, Rae, Mphele, Matloga (Kalake 64'), Khwela, Mothobi, Garcia, Mathibe, Boke (Kgatla 76')