In the first match back after a three-week break for international fixtures, both sides scored two tries apiece but five penalties to Aaron Cruden proved the difference in a tightly contested New Zealand derby.
The win puts the Chiefs in prime position to top the New Zealand conference, although they face a tough final two regular season matches against the Crusaders and Hurricanes.
The Highlanders entered the match eighth on the ladder and, barring major upsets, have no chance of achieving a top six play-off position.
"It's not easy to get a win down in Dunedin," Chiefs captain Craig Clarke said.
"What pleased me the most was probably the heart of our defence towards the end when they were chasing the game, we just stayed in there and made some tackles."
The Chiefs stunned the Highlanders with a try in the opening two minutes, Liam Messam intercepting a pass and sending Sonny Bill Williams down the field, with Tim Nanai Williams touching down for the five pointer.
Cruden converted but the Highlanders, their season on the line, continued to attack, earning two penalties to one to narrow the gap to 10-6 after 20 minutes.
They patiently dominated possession but only managed to secure a penalty before conceding against the run of play three minutes before half-time after a charge down by Ben Tameifuna led to a Robbie Robinson try.
Cruden piled on the pressure with a penalty after the half-time siren, then another just after the restart to make it 21-9.
The hosts made the most of an attacking opportunity when Sonny Bill Williams was penalised for a shoulder charge, rewarded when they opted to run the ball and hooker Andrew Hore forced the ball over from a ruck.
The Chiefs responded with a period of sustained attack but had a try disallowed when the ball was ruled held up over the line, only for the Highlanders' Adam Thomson to concede a penalty and make it 24-14.
Hosea
Gear managed a try for the Highlanders three minutes from time but the
Chiefs defence proved up to the task of keeping them out.
Highlanders:
15 Ben Smith, 14 Kade Poki, 13 Tamati Ellison, 12 Phil Burleigh, 11 Hosea Gear, 10 Chris Noakes, 9 Aaron Smith, 8 Nasi Manu, 7 Tim Boys, 6 Adam Thomson, 5 Nick Crosswell, 4 Jarrad Hoeata, 3 Ma'afu Fia, 2 Jason Rutledge, 1 Jamie Mackintosh (captain)
Substitutes: 16 Andrew Hore, 17 Chris King, 18 Josh Bekhuis, 19 James Haskell, 20 Jimmy Cowan, 21 Mike Delany, 22 Buxton Popoali'i.
Chiefs:
15 Robbie Robinson, 14 Tim Nanai-Williams, 13 Jackson Willison, 12 Sonny Bill Williams, 11 Asaeli Tikoirotuma, 10 Aaron Cruden, 9 Tawera Kerr-Barlow, 8 Kane Thompson, 7 Tanerau Latimer, 6 Liam Messam, 5 Brodie Retallick, 4 Craig Clarke (captain), 3 Ben Tameifuna, 2 Mahonri Schwalger, 1 Toby Smith
Substitutes: 16 Hika Elliot, 17 Sona Taumalolo, 18 Michael Fitzgerald, 19 Sam Cane, 20 Brendon Leonard, 21 Andrew Horrell, 22 Lelia Masaga