The Bloemfontein-based Cheetahs, winless and bottom of the standings before the match, sealed the sensational upset through second-half tries from Phillip Snyman and Sarel Pretorius.
It was magnificent defence and dominance of the breakdown that laid the groundwork for the win, however, blunting the Waratahs' much-vaunted attack and disrupting any momentum the home side generated.
"We're absolutely delighted, the guys knew it would take a special effort to get our first win overseas," said Cheetahs lock Wilhelm Steenkamp.
"We spent a lot of time analysing their game and we got the result of it."
Already without regular skipper Phil Waugh and hooker Tatafu Polota-Nau, the Waratahs lost Wallaby prop Benn Robinson and returning number eight Wycliff Palu in the first half.
Poor handling in greasy conditions, a malfunctioning line-out and a bloodless effort at the breakdown added to their woes and they were booed off the pitch after what was a humiliating reverse for a team with title ambitions.
"We just didn't perform basically, it's disappointing obviously," said stand-in Waratahs captain Dean Mumm.
"All credit to their defence, they didn't allow us to play the way we wanted to. They fronted up very well and we didn't respond."
Centre Sias Ebersohn kicked two penalties to one from Wallaby fullback Kurtley Beale to give the Cheetahs a 6-3 halftime lead and he added another five minutes into the second half to extend the advantage.
The Waratahs still looked to have plenty of time to get back into the game, however, when flyhalf Berrick Barnes kicked the ball across the field towards winger Drew Mitchell in the 58th minute.
The ball was intercepted by Cheetahs fullback Frans Viljoen who flicked the ball to Pretorius and the scrumhalf set off down the touchline before feeding Snyman who outpaced the cover defence to touch down, Ebersohn adding the extra two points.
Again, the Waratahs tried to rally but the mistakes continued and their hopes had all but vanished when scrumhalf Pretorius reached through a pile of bodies to secure the victory two minutes before the whistle.
"We can be very proud of how we played, we fought until the end," said Springbok openside flanker Heinrich Brussow, who had an outstanding match in his first start since returning from a year out injured.
Scorers:
Waratahs - Penalty: Kurtley Beale.
Cheetahs - Tries: Phillip Snyman, Sorel Pretorious. Conversions: Sias Ebersohn (2). Penalties: Ebersohn (3).
Referee: Chris Pollock (NZL)
Teams:
Waratahs:
15. Kurtley Beale, 14. Afa Pakalani, 13. Lachlan Turner, 12. Tom Carter, 11. Drew Mitchell, 10. Berrick Barnes, 9. Luke Burgess, 8. Wycliff Palu, 7. Pat McCutcheon, 6. Ben Mowen, 5. Kane Douglas, 4. Dean Mumm (captain), 3. Al Baxter, 2. John Ulugia, 1. Benn Robinson
Substitutes: 16. Damien Fitzpatrick, 17. Sekope Kepu, 18. Sitaleki Timani, 19. Dave Dennis, 20. Brendan McKibbin, 21. Daniel Halangahu, 22. Ryan Cross
Cheetahs:
15. Riaan Viljoen, 14. Phillip Snyman, 13. Robert Ebersohn, 12. Andries Strauss (captain), 11. Fabian Juries, 10. Sias Ebersohn, 9. Tewis de Bruyn, 8. Ashley Johnson, 7. Phillip van der Walt, 6. Heinrich Brussow, 5. Wilhelm Steenkamp, 4. Martin Muller, 3. WP Nel, 2. Ryno Barnes, 1. Coenie Oosthuizen
Substitutes: 16. Skipper Badenhorst, 17. Lourens Adriaanse, 18. Frans Viljoen, 19. Kabamba Floors, 20. Francois Uys, 21. Sarel Pretorius, 22. Naas Olivier