The Bulls led 21-7 early in the second half at Loftus Versfeld on Saturday but tries to Kurtley Beale and Curtis Rona put the Waratahs in position to secure a valuable away win and a share of top spot in the Australian conference.
But a try to loosehead prop Simphiwe Matanzima with ten minutes to play put the Bulls back on top for good to see the Waratahs fall behind the Rebels, Brumbies and Reds in the chase for a semi-final berth.
The Waratahs produced a spirited second-half performance but they were unable to conjer up a match-winning score, leaving them with a must-win clash against the Lions in Johannesburg next Saturday night as they battle to remain in contention for the playoffs.
"We certainly put a lot of pressure on the Bulls, they were strong enough to hold us out there a lot of times," captain Michael Hooper said after the match.
"We got a couple of big line breaks, they chased us down and managed to slow up the ball."
Hooper became the most capped Waratahs captain in Super Rugby, leading out his side for the 57th time.
The visitors found themselves 10-0 down inside of 10 minutes when the Bulls followed up a Pollard penalty goal with a try to fullback Warrick Gelant.
A converted try to Nick Phipps appeared to steady the Waratahs but the veteran halfback's fortunes turned when Bulls No.8 Duane Vermeulen swooped from a lineout for an intercept try, brushing off winger Rona's cover defence to finish off a determined 60-metre run.
While the visitors pressed for a second try before halftime, the Bulls' defence stood firm and Pollard drilled a penalty from inside his own half for an 18-7 edge at the main break.
Pollard slotted his third penalty within minutes of the restart to extend the lead but the Waratahs struck back in the 51st minute from a scrum deep in Bulls territory, Beale evading three defenders to score near the posts.
Foley's conversion closed the gap to seven points before the visitors missed an excellent opportunity to level the scores on the hour mark, Rona unable to complete a sweeping 75-metre sequence after losing possession as he reached for the tryline.
But the winger made no mistake five minutes later for the Waratah's third try, Foley landing a tricky conversion to level the game.