The Waratahs recovered from a terrible start and the loss of Berrick Barnes to a suspected fractured wrist to lead at half-time for the first time in this season's tournament, but wing Raymond Rhule scored his second try late on to clinch it for the Cheetahs.
Robert Ebeshohn also touched down for the Cheetahs, with Johan Goosen adding three conversions and two penalties to his growing haul.
Peter Betham and Adam Ashley-Cooper crossed in the first half for the Waratahs, who have now lost three straight times to the Cheetahs and have a single win from four matches this season.
"We probably took it a little bit for granted in the second half," Waratahs captain Dave Dennis said. "We knew at half-time we were on top of them and we just couldn't execute in that second half."
The Cheetahs, on the other hand, will head to the Western Force next weekend just short of the wildcard berths and chasing a third away win.
"The guys showed a lot of guts," Cheetahs captain Adriaan Strauss said. "We were quite tired out there and everyone just got up off the deck and worked hard."
The Bloemfontein-based outfit got off to a flying start, scoring inside the first minute. Barnes sent down a long kick that Willie Le Roux ran back and chipped over the first line of opposition.
It was 7-6 when Brendan McKibbin slotted a pair of penalties but the Cheetahs touched down again midway through the first period. They quickly worked the ball wide left from a turnover and, although Rhule was brought down just short, he still managed to reach out and score while on the ground.
At 14-6 down and with Barnes replaced in pain after tackling giant lock Lodewyk De Jager, it looked all over for the Waratahs, who made six changes after last week's mauling by the ACT Brumbies. But the Cheetahs seemed to tire dramatically after their multiple phases and hard running failed to yield more points.
Betham touched down and Ashley-Cooper scored his first try in 16 Super Rugby matches, placing the ball in a second movement while on the deck. Referee Garratt Williamson awarded the try after consulting with his TV official that the ground was good and that there had been no obstruction in the build-up by the decoy runner.
That made it 20-17 to the home side at the break and, despite another injury-enforced change when prop Benn Robinson went off with a concussion after lining up for the second period, the Waratahs still led by three at the start of the final quarter.
They were caught out by another chip from Le Roux, making the yards and flipping his catch to Rhule on his shoulder.
Although the wing was stopped, the Cheetahs recycled through a couple more phases and Rhule rushed on an angle to exploit a gap in the tiring home defence and score.
The conversion made it 27-23 and all the Waratahs could muster in response was a another penalty by McKibbin.