The Chiefs ended the Sharks unbeaten run with a 15-9 home victory in Hamilton in a match which was decided by the boot.
The victory is the Chiefs second victory at home this season after they lost to the Hurricanes last weekend in Wellington.
The Sharks retained their place at the top of the Super Rugby standings - with matches still to come - and extended their lead as they secured a losing bonus point taking them to 19 points on the overall table.
The Durban-based Sharks won their first four matches, posting their first-ever back-to-back wins in Australia but failed to improve on a 40 percent winning record in New Zealand.
Only the Stormers who have played two games less than the Sharks remain unbeaten in this season's tournament.
The Sharks led 3-6 at half time but the Chiefs came out for the second half with a much greater intensity which forced the Sharks into conceding penalties.
Replacement flyhalf Mike Delany came on for Stephen Donald and kicked four penalties during the second half which secured the victory for the Chiefs.
For most of the match the championship-leading Sharks looked the better team but were unable to take advantage of a steady stream of Chiefs' errors.
Though they also defended superbly, Delany's goalkicking consigned them to defeat.
The Sharks were due to fly home to South Africa hours after the match and will then fly to London on Thursday to meet the Crusaders at Twickenham Stadium on Sunday in the first Super rugby match played outside the southern hemisphere.
The match has been moved to London because the Crusaders' home ground at Christchurch was wrecked in last month's deadly earthquake.
By Friday more than 30,000 tickets to the London match had been sold.
The Chiefs continuity was wrecked by handling errors but they grafted throughout and secured their second win in five matches this season.
The Chiefs paid a heavy injury price for their win, losing Donald to a back injury during the first half.
The seriousness of the injury was not immediately clear but the flyhalf - recent understudy to All Blacks star Daniel Carter - was taken to hospital for examination.
Prop Ben May suffered a serious calf strain and replacement lock Romana Graham an apparent concussion, adding to Waikato's already heavy injury toll ahead of next week's match against the Auckland Blues.
Sharks flyhalf Patrick Lambie, who entered the match as the tournament's leading pointscorer this season with 65 points, added to that tally with two first half penalties.
He slotted goals in the fourth and 27th minute while fullback Tim Nanai-Williams kicked a goal for the Chiefs while Donald was receiving treatment for his injury.
Delany then came on and wrested the match from the Sharks. He kicked long-range goals in the 41st and 46th minutes to give the Chiefs the lead, then added two late goals after Lambie had equalized in the 53rd minute.
The Sharks mammoth forward pack dominated the Chiefs for the most of the match, with Springboks hooker Bismarck du Plessis playing a provocative role.
The Chiefs managed to stay in the match through resolute defense and took the win by exploiting field position in the second half.
Final Score Chiefs 15 Sharks 9
Pen - T Nanai-Williams, M Delany 4
Pen -P Lambie 3
Referee: Garratt Williamson
Assistant Ref 1:Kane McBride
Assistant Ref 2:Nick Briant
Chiefs :1. Ben May,2. Hika Elliot,3. Nathan White,4. Craig Clarke,5. Isaac Ross,6. Scott Waldrom,7. Tanerau Latimer,8. Liam Messam (Captain),9. Brendon Leonard,10. Stephen Donald,11. Sitiveni Sivivatu,12. Tana Umaga,13. Richard Kahui,14. Lelia Masaga,15. Tim Nanai-Williams
Reserves:16. Aled de Malmanche,17. Sona Taumalolo,18. Romana Graham,19. Fritz Lee,20. Taniela Moa,21. Mike Delany,22. Dwayne Sweeney
Sharks :1. John Smit ( Captain ) , 2. Bismarck du Plessis , 3. Jannie du Plessis , 4. Steven Sykes , 5. Alistair Hargreaves , 6. Keegan Daniel , 7. Willem Alberts , 8. Ryan Kankowski , 9. Charl McLeod , 10. Patrick Lambie , 11. Lwazi Mvovo , 12. Meyer Bosman , 13. Stefan Terblanche , 14. Odwa Ndungane , 15. Louis Ludik
Replacements , 16. Craig Burden , 17. Tendai Mtawarira , 18. Anton Bresler , 19. Jacques Botes , 20. Conrad Hoffmann , 21. Jacques-Louis Potgieter , 22. Adrian Jacobs