The Stormers were denied crucial points in Melbourne on Friday as a controversial penalty try handed the Rebels a 30-21 victory at AAMI Park.
The result is the Rebels' first victory over South African opposition and leaves the Stormers' hopes of qualifying for the play-offs in tatters.
In the dying minutes, with the Stormers leading 21-10, TMO Matt Goddard chose to ignore what appeared to be a clear knock-on and instead ruled that Martin Bezuidenhout had prevented a Rebels try by holding back replacement scrum-half Nick Phipps.
And things went from bad to worse for last season's SA Conference winners as Rebels full-back Jason Woodward - who kicked 15 points - slotted a 78th minute penalty to send the Stormers back to Cape Town empty handed.
The Stormers led 14-13 at half time in a ding-dong battle that saw the lead change hands five times.
The Rebels took an 10-0 lead early on thanks to a try from close range from number eight Scott Higginbotham and a penalty from Woodward.
The Stormers closed the gap on the 15-minute mark however when scrum-half Louis Schreuder slipped out of a tackle and then zigzagged past a handful of defenders to score.
The visitors moved in front after half an hour when lock Eben Etzebeth bust clear after a pass from Elton Jantjies before finding a flying Bryan Habana up in support and the veteran wing sailed over for his first try of the season.
Joe Pietersen converted both tries but Woodward landed his second penalty on the stroke of half time to cut the deficit to a single point as the teams headed for the changing rooms.
The home side were first to strike after the break though as lock Hugh Pyle ran onto a pass from Phipps to crash over after Higginbotham broke through the middle of a ruck. Woodward added the extras to put the Rebels 20-14 up just before the hour mark.
A break from Habana was at the origin of the Stormers' third try, scored out wide by Andriess Bekker after a pass from his second row partner Etzebeth. Pietersen was on target again to put the Stormers back in front at 21-20 and set up a nail-biting final quarter.
The late drama would follow as Bezuidenhout collected a chip ahead from Higginbotham. The Rebels skipper tackled the Stormers hooker, knocking the ball forward and out of Bezuidenhout's hands in the process. Phipps hacked the ball ahead and bolted for the tryline, only to have his jersey tucked as the Stormers scrambled back.
For the Rebels:
Tries: Higginbotham, Pyle, Penalty try
Cons: Woodward 3
Pens: Woodward 3
For the Stormers:
Tries: Schreuder, Habana, Bekker
Cons: Pietersen 3
Yellow card: Bezuidenhout
Rebels 15 Jason Woodward, 14 Tom English, 13 Mitch Inman, 12 Rory Sidey, 11 Lachlan Mitchell, 10 Bryce Hegarty, 9 Nic Stirzaker, 8 Scott Higginbotham, 7 Scott Fuglistaller, 6 Jarrod Saffy, 5 Cadeyrn Neville, 4 Hugh Pyle, 3 Laurie Weeks, 2 Ged Robinson, 1 Nic Henderson.
Replacements: 16 Shota Horie, 17 Paul Alo-Emile, 18 Luke Jones, 19 Gareth Delve, 20 Jordy Reid, 21 Nick Phipps, 22 Kimaumi Sitauti.
Stormers: 15 Joe Pietersen, 14 Gio Aplon, 13 Juan de Jongh, 12 Jean de Villers, 11 Bryan Habana, 10 Elton Jantjies, 9 Louis Schreuder, 8 Nizaam Carr, 7 Siya Kolisi, 6 Deon Fourie, 5 Andriess Bekker, 4 Eben Etzebeth, 3 Pat Cilliers, 2 Martin Bezuidenhout, 1 Steven Kitshoff.
Replacements: 16 Brok Harris, 17 Frans Malherbe, 18 Gerbrandt Grobler, 19 Don Armond, 20 Nic Groom, 21 Gary van Aswegan, 22 Gerhard van den Heever.
Venue: AAMI Park, Melbourne
Referee: Mike Fraser (New Zealand)
Assistant referees: Rohan Hoffmann (Australia), Ed Martin (Australia)
Television match official: Matt Goddard (Australia)