Charlie Ngatai scored in the corner at Waikato Stadium with 11 minutes remaining to put the Chiefs back at the head of the pack, replacing the Highlanders who had led after a surprise bonus-point win over the Blues last week.
But there will be serious questions asked in the Chiefs camp as they struggled for possession and trailed 7-16 at half-time against a side with a reputation as the weakest New Zealand franchise.
Although the Chiefs led briefly in the first half it took until the second spell before they were able to gain a measure of control against a side containing mainly unknowns at Super Rugby level.
Even then, as they started to get an even share of possession and territory, they still struggled to breach the Highlanders' defence.
Three penalties and a conversion by Lima Sopoaga coupled with a try to John Hardie from a line-out drive gave the Highlanders command in the first half after the Chiefs scored early with a try to Tim Nanai-Williams converted by Aaron Cruden.
The Chiefs narrowed the gap to two points soon after the resumption when they wore down the Highlanders' defence with a series of close drives at the line which culminated in a try to Liam Messam, again converted by Cruden.
Yet the Highlanders would not lie down. A solo burst by hooker Liam Coltman took the visitors deep into Chiefs territory where Sopoaga landed his fourth penalty to take them to a 19-14 lead.
However, their hopes of staying in front were dashed when replacement loose forward Liam Squire, making his Super rugby debut, led the Chiefs deep into Highlanders territory where Cruden chipped into the right corner for Ngatai to score the match-winning try.
ScorersChiefs - Tries: Tim Nanai-Williams, Liam Messam, Charlie Ngatai. Conversions: Aaron Cruden (3)
Highlanders - Try: John Hardie. Conversion: Lima Sopoaga. Penalties: Sopoaga (4)
Teams:Chiefs
15 Mils Muliaina, 14 Tim Nanai-Williams, 13 Robbie Fruean, 12 Charlie Ngatai, 11 Asaeli Tikoirotuma, 10 Aaron Cruden (captain), 9 Tawera Kerr-Barlow, 8 Liam Messam, 7 Tanerau Latimer, 6 Nick Crosswell, 5 Matt Symons, 4 Michael Fitzgerald, 3 Ben Tameifuna, 2 Mahroni Schwalger, 1 Pauliasi Manu
Substitutes: 16 Rhys Marshall, 17 Jamie Mackintosh, 18 Josh Hohneck, 19 Tevita Koloamatangi, 20 Liam Squire, 21 Brad Webber, 22 Andrew Horrell, 23 James Lowe
Highlanders
15 Ben Smith (co-captain), 14 Richard Buckman, 13 Winston Stanley, 12 Shaun Treeby, 11 Malakai Fekitoa, 10 Lima Sopoaga, 9 Aaron Smith, 8 Nasi Manu (co-captain), 7 John Hardie, 6 Gareth Evans, 5 Joe Wheeler, 4 Jarrad Hoeata, 3 Chris King, 2 Liam Coltman, 1 Kane Hames
Substitutes:16 Brayden Mitchell, 17 Matias Diaz, 18 Craig Millar, 19 Josh Bekhuis, 20 Shane Christie, 21 Fumiaki Tanaka, 22 Trent Renata, 23 Phil Burleigh