NSW Waratahs' Super Rugby finals hopes are hanging by a thread following a gut-wrenching one-point loss to the Lions in Johannesburg.

The Waratahs led late before a Shaun Reynolds penalty goal in the 68th minute secured the Lions a 29-28 victory on Sunday.

NSW's sixth bonus-point defeat in a 2019 campaign of near misses leaves the Waratahs languishing in 13th place on the ladder and seven points adrift of Australian conference leaders the Melbourne Rebels.

Leading 21-19 at the break after three slick first-half tries to Nick Phipps, Michael Hooper and Rob Simmons, the Waratahs were unable to shake the Lions.

Runners-up for the past three seasons, the free-running South Africans hit the front for the first time four minutes into a frenetic second half with their third try of their own, through Springboks winger Courtnall Skosan.

But unlike last year's semi-final capitulation in Johannesburg, the Tahs refused to fold. The visitors regained the lead when Tom Staniforth crashed over in the 57th minute, only for Reynolds to have the final say.

"I thought it was a really good contest; back and forth tries, some really exciting rugby and down to the wire there with both teams getting opportunities," said Waratahs captain Hooper.

Despite slipping further behind the Rebels, who stretched their lead atop the Australian conference with a 30-24 win over Queensland Reds on Friday night, Hooper wasn't giving up hope of making the finals.

The Waratahs won't return to Australia empty-handed, having picked up two bonus important points in their narrow losses on the Highveld to the Lions and Bulls.

"Every point counts. We managed to walk away with another one, just short of a win, which is what we desperately wanted today," Hooper said.

"Of course it's better than nothing. We want to build some momentum. We were unable to do that today. But there's so much fight in this team."

The Waratahs take on the Reds next Saturday in Brisbane in a must-win encounter for both teams.