The Bulls disrupted the Waratahs charge for the play offs on Saturday beating them by 16 points to 13 at Loftus Versfeld.
The Waratahs had been favourites to win the match and they will be disappointed to only pick up a bonus point.
The Bonus point however moved the Waratahs from third to second on the points table.
The match conditions were far from ideal and both teams resorted to drop goals to score points with the Bulls using the tactic twice.
This was the Bulls second consecutive win after they beat the Highlanders two weeks ago and one that will go a long way in lifting the Bulls to mid table by the end of the competition.
The greasy underfoot conditions and endless unexpected rain made proceedings tricky for both sides with none being able to throw the ball around.
However the forward battle was extremely bruising with the Bulls holding the upper hand over the Waratahs.
The Bulls should have picked up at least one more try but they were let down by their poor handling in the wet conditions.
In hindsight, this victory will not only go a long way in ensuring that the Bulls regain some credibility in the competition as defending champions, after almost slipping to 14th place, but the win could secure semifinal berths for compatriots the Stormers and Sharks in the next coming weeks, barring losses for both sides.
The Waratahs started the game in a manner typical of a team hellbent on cementing second place on the log when Rob Horne silenced the small crowd at Loftus with a try in the 8th minute.
The visitors could have extended their lead in the 17th minute were it not for some heart stopping defence from the Bulls with prop Werner Kruger's well timed desperate tackle knocking the ball out of Luke Burgess' hand over the tryline.
Two minutes later the Bulls collected their first points through a snap drop-goal from replacement flyhalf Derick Hougaard. On the half hour mark and with the hosts enjoying hordes of possession Morne Steyn slotted over a penalty to bring the Bulls within a solitary point of the Waratahs.
The Bulls could have gone into the half-time interval with a slender two point lead but Steyn's penalty kick came off the upright.
The Bulls continued to throw men behind the ball in the second half and they were rewarded when hooker Derick Kuun scored a try engineered from a turnover in the Bulls half in the 44th minute.
With the Bulls leading 13-7, the Waratahs fought back in difficult conditions through their flyhalf Kurtley Beale who slotted over a penalty in the 54th minute followed by a freakish drop-goal in the 64th minute which leveled the scores at 13-all.
The Bulls are renowned masters of the kicking game and with kicking seemingly the only way to gather points it was the Bulls that won the game with seven minutes left on the clock when Steyn slotted over a drop-goal from close range to see the Bulls now rise to 10th place on the Super 14 log.
Drop - Derick Hougaard, Morne Steyn
Drop - Kurtley Beale
Loftus Versfeld, Pretoria
Referee: Lyndon Bray (New Zealand)
Touch judges: Brent Murray (New Zealand), Pro Legoete (South Africa)
TMO: Michael Cupido (South Africa)
Zane Kirchner, Akona Ndungane, JP Nel, Wynand Olivier, Bryan Habana, Morne Steyn, Francois Hougaard, Pierre Spies, Wikus van Heerden (capt.), Deon Stegmann, Wilhelm Steenkamp, Bakkies Botha, Werner Kruger, Derick Kuun, Gurthro Steenkamp.
Reserves: Bandisa Maku, Jaco Engels, Rayno Gerber, Danie Rossouw, Fourie du Preez, Derick Hougaard, Pedrie Wannenburg.
15. Sam Norton-Knight
Reserves: 16. Adam Freier, 17. Matt Dunning, 18. Will Caldwel , 19. David Lyons, 20. Sekope Kepu, 21. Matt Carraro
22. Brett Sheehan