South African conference leaders the Lions have suffered a rare streak of three Super Rugby losses after they went down to the Highlanders 39-27 in Dunedin on Saturday night.

The Highlanders held off a late charge by the Lions to extend their home winning streak to 11 matches and leave the South Africans still chasing their first victory over New Zealand opponents this season.

The Highlanders raced out to a 19-3 lead at Forsyth Barr Stadium, with Lima Sopoaga crossing from close range, Liam Coltman crashing over and Luke Whitelock also bagging a try.

But the Johannesburg-based team hit back with two quick tries to cut the lead to 19-15 at halftime.

Their rolling maul was especially effective and hooker Robbie Coetzee crossed for his second five-pointer early in the second half.

The Highlanders then put the foot down, with Waisake Naholo and Teihorangi Walden tries creating a handy buffer.

But the Lions pulled within six points when Elton Jantjies converted Marnus Schoeman's 73rd-minute try.

"We thought we were going pretty good at halftime," Highlanders captain Ben Smith said in a post-match interview.

"The Lions are a good team... they've got a pretty good lineout and some big physical forwards that took us on."

After humiliating the Waratahs in Sydney on April 20 with a 29-0 triumph, the Lions lost to Queensland and the Hurricanes in a tough road trip.

Nonetheless, last season's beaten finalists retain top spot in the South African conference, seven points ahead of Argentina's second-placed Jaguares, but queries remain over their title credentials as their struggles against New Zealand sides continue.

The Lions were upset 25-17 in the title decider at their Ellis Park home last year by the Crusaders and have not tasted victory against a New Zealand team since.