Lima Sopoaga, Liam Coltman, Luke Whitelock, Waisake Naholo and Teihorangi Walden scored tries for the home side, who grabbed their seventh win for the season to keep their playoffs hopes alive.
Robbie Coetzee touched down either side of halftime for the Lions, who pulled to within six points of the home side when Elton Jantjies converted Marnus Schoeman's 73rd minute try.
However, Sopoaga slotted a penalty minutes later to stretch the lead to nine points before kicking another in the final seconds to finish with 19 points for the game.
Beaten by the Sharks in their last start in Durban, the Highlanders were glad to return to their Forsyth Barr stronghold, where they notched their 11th win in succession.
They stormed to a 19-3 lead in the 34th minute after Whitelock grabbed the team's third try but the Lions rallied to within four points by halftime.
"We thought we were going pretty good at halftime. The Lions are a good team and they put pressure on us in that last 10 minutes of that first half," Highlanders captain Ben Smith said in a post-match interview.
"They've got a pretty good lineout and some big physical forwards that took us on."
The Lions' trip to Australia and New Zealand finished on a sour note with their third successive loss following defeats to the Wellington Hurricanes and Queensland Reds.
They retain top spot in the South Africa 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 Canterbury Crusaders and have not tasted victory against a New Zealand team since.
(Reporting by Ian Ransom in Melbourne; Editing by John O'Brien)
