The Rebels had looked on course for a first win over their fellow Australians when Ged Robinson's try helped them to take a half-time lead in Sydney.
However, , Michael Hooper and Paddy Ryan scored second-half tries to give the Waratahs their first Super Rugby win since a 30-21 victory over the same opponents in April last year.
Kurtley Beale touched down in the final minute to earn the Rebels a losing bonus point and his fellow Wallabies back James O'Connor converted to complete a personal haul of 16 points.
Brendan McKibbin kicked the home side's other 16 points before limping off with some seven minutes left.
The Rebels have lost two of three matches this season but the Waratahs look to be heading the right way after two games.
Although the Waratahs' second-half performance suggests they should at least challenge for a place in the end-of-season playoffs, they were unable to gain a foothold in the first half on a rain-lashed pitch.
The Rebels' breakthrough came after Tatafu Polota-Nau was yellow-carded for repeatedly offending at the breakdown.
The ball was popped back to Robinson from a smart short lineout move and the hooker went over unopposed in the corner.
"We probably made it hard for ourselves but we kept playing," Waratahs captain Dave Dennis said. "It was poor discipline really. We had to keep backing ourselves and not look at the scoreboard."
O'Connor's conversion made it 13-3 and an exchange of penalties between O'Connor and McKibbin meant it was 16-6 at the interval.
Foley crossed following a break created by Kane Douglas, Hooper rounded off a slick passing move to put the home side ahead and Ryan pumped his way through a tackle to go over from close range and score his first try in Super Rugby.
Blues 34-15 Crusaders
The Auckland Blues took apart the Canterbury Crusaders in a thumping 34-15 win on Friday, outscoring their illustrious New Zealand rivals by five tries to none at Eden Park.
Steven Luatua touched down before wing Frank Halai scored two tries for the second time in two matches to put the home side 20-6 ahead against the seven-time champions.
Dan Carter hauled the Crusaders to within five points at the start of the second half with his fifth penalty but the Blues, who finished bottom of the New Zealand standings last year, stood firm.
Flanker Luke Braid crossed to give the home side a bonus point and wing George Moala scorched past four Canterbury defenders with six minutes left to touchdown and put the gloss on the impressive performance.
The Crusaders were extremely rusty after a first-round bye,uncertain under the high ball and - with New Zealand captain Richie McCaw on a six-month sabbatical - uncharacteristically vulnerable at the breakdown.
The Crusaders did improve in the final quarter but Israel Dagg was denied a crucial try in the left corner before Auckland's late flurry. The television referee ruling that the All Black wing failed to release the ball in a tackle before crossing.
It was the Blues' second bonus point win following a first-round victory in Wellington last week and firmly places John Kirwin's side among the contenders for a title they have not won wince 2003.
"We created opportunities for ourselves out wide," Bluesscrumhalf Piri Weepu said in a pitchside interview. "But we've got to be a little bit tighter around our defence."
Weepu was erratic with his kicking but he laid on Luatua's opening try before Halai scored twice in the right-hand corner.
His first try came after the Blues recycled the ball near the left corner flag and spread it quickly across the line, while his second was down to quick thinking from flyhalf Chris Noakes, who chipped the ball over the top to him.
Carter dragged the Crusaders to within eight points at theinterval and trimmed the deficit further at the start of the second period, but Braid picked up and went over from a yard from an opening that came from another spilled high ball by the visitors.
And moments after Dagg was denied a score that would have given Carter a shot at making the score 27-22 with eight minutes left, Moala raced away to send the home fans wild.
Reds 18-12 Hurricanes
The Queensland Reds withstood a late Wellington Hurricanes' onslaught to win 18-12 and maintain their strong recent record against New Zealand teams.
Wallabies wing Digby Ioane scored his first try in Brisbane since the 2011 final and lock Rob Simmons touched down for the first time in 51 Super Rugby appearances to give the Australian outfit a deserved victory.
Quade Cooper kicked the Reds' remaining eight points but the Hurricanes almost staged a late comeback, dominating possession in the final 10 minutes and mounting repeated raids on the home side's line.
The Reds nearly threw away a ninth victory in 10 matches against New Zealand opposition when Cooper hurled the ball back across his own line with five minutes left but the visitors' try was ruled out by the TV official for a knock on in the build-up.
The Hurricanes ended a game try-less for the first time since their last match of the 2011 season, only troubling the scoreboard with four penalties from fly-half Beauden Barrett, who twice struck the post and missed a total of three place kicks.
"We were playing in our own half and against a quality side like the Hurricanes you can't do that," Reds captain James Slipper said. "The defence we put up there was phenomenal."
A 23rd win from their last 26 home games means the Reds head into next week's game with the Melbourne Rebels in good spirits.
The winless Hurricanes must hope home advantage helps them avoid a backlash from a Canterbury Crusaders side soundly beaten 34-15 by the Auckland Blues earlier on Friday.
Barrett had put the Hurricanes 9-6 ahead before Ioane finally ended his barren streak midway through the first half, taking a low, flat pass and diving for the left corner.
Cooper's missed conversion meant it was 11-9 at halftime.
Eight minutes after the restart, the Reds worked the ball to within striking distance from a scrum turnover and Simmons picked up to dive over from close range.
Cooper converted and, while Barrett struck his fourth penalty, the Hurricanes' laboured in vain for a try.