The Bulls, who received little reward for a reasonable effort by the forwards, nearly denied the home side the bonus point when Dries Swanepoel went over with seven minutes to go.
But prop Angus Ta'avao scored in the final move of the match to hand the Waratahs their fourth try and a much-needed bonus point that takes them to the top of the Australian conference on 30 points after 10 games, one ahead of the Brumbies, who have played an extra match.
Star Waratahs playmaker Kurtley Beale - who announced this week that he will be joining English club Wasps on a two-year deal at the end of the Super Rugby season - sustained what appeared to be a serious knee ligament injury after just 40 seconds, which was a big blow to the Australian outfit.
Beale had gone up to contest a high ball, but his left boot appeared to stick into the turf and then gave way, and he was left clutching his left knee while in considerable pain. A stretcher had to be brought on to take him off the field.
Both teams battled to get their games going, with the 'Tahs missing Beale's significant influence on their attacking play as they resembled a disjointed unit.
Strike-runner Israel Folau was hardly utilised, as he usually feeds off Beale's stepping and offloads in the tackle. Instead, flyhalf Bernard Foley and fullback Andrew Kellaway made liberal use of the boot, while the Bulls weren't much better either in the opening stanza.
They had just two half-chances to score, when centre Jan Serfontein cut the line and fullback SP Marais repeated the feat, but Adriaan Strauss' side couldn't finish off those opportunities.
Foley missed an eighth-minute penalty, but the deadlock was broken at last after 34 minutes when the 2014 champions managed to breach the Bulls defence off a scrum on the 22m line, with Foley making a half-break before No 8 Wycliff Palu punched a hole up the middle. It created the gap for scrumhalf Nick Phipps to dart through, and even though he was stopped by locks Jason Jenkins and RG Snyman, he wasn't held on the ground and slithered his way over.
The Bulls scrum appeared to be dominant for most of the first 40 minutes, despite New Zealand referee Glen Jackson penalising them more often than he did the Waratahs.
Tighthead prop Marcel van der Merwe, especially, gave Paddy Ryan a working over, and the Bulls were rewarded in the final minute before the break with a penalty that was slotted from about 40 metres from flyhalf Tian Schoeman.
But after some strong words from coach Daryl Gibson in the change room, the Waratahs resembled the team that won the title two years ago as they put together 15 phases of relentless attack, and Phipps drew the final defender and put flank Dean Mumm over after four minutes in the second half.
After Foley stretched the lead with a three-pointer, the Bulls managed to hold on to the ball a bit better, and they went through 11 phases as Jesse Kriel played a more prominent role on attack, and the big forwards such as Snyman and Roelof Smit carried strongly. But Kriel was brought down five metres out, and Folau won the breakdown penalty to deny the Bulls in the 60th minute.
The South Africans held out for another 10 minutes, but it was Folau who finally made a contribution on attack as he burst through the defence and found Phipps on his inside to end any hopes of a late comeback from the Pretoria side. With the result decided, the Waratahs fell off a few tackles and the Bulls muscled the ball up for over 10 phases again, and this time they got over the whitewash as replacement centre Swanepoel rounded off smartly.
That meant that the Waratahs needed to score once more to get a bonus point, and when Bulls blindside flank Jannes Kirsten was yellow-carded for a collapsing a maul five metres from his line, the Aussies took a quick tap penalty and replacement prop Ta'avao powered over.
The defeat ends a disappointing tour for the Bulls, who started promisingly by beating the Force in their first match in Australia, but went down to the Brumbies last week.
They now travel home to take on the Stormers at Loftus Versfeld next Saturday. SCORERS Waratahs: 31 -Tries: Nick Phipps (2), Dean Mumm, Angus Ta'avao. Conversions: Bernard Foley (4). Penalty: Foley (1). Bulls: 8 - Try: Dries Swanepoel. Penalty: Tian Schoeman (1). - African News Agency (ANA)
Original source: Bulls lose last tour match