Three successive defeats had made for a miserable trip for the Stormers but a brilliant individual try from pay winger Dillyn Leyds in the third minute gave them early hope of returning to Cape Town with a fourth win of the season.
Five tries, including two from winger Ruhan Nel, played a big part but the victory was built on a huge defensive effort from the tourists at the Melbourne Rectangular Stadium.
"I think the boys were really fired up and they put their bodies on the line tonight," said Steven Kitshoff, standing in as Stormers captain for the rested Siya Kolisi.
"I think it was an unbelievable effort from forwards and backs."
A Jean-Luc du Plessis penalty helped give the Stormers a 10-3 lead at halftime but Rebels fullback Reece Hodge intercepted a pass for a converted try that levelled up the scores straight after the break.
The home crowd expected the Rebels' much vaunted backline, which had until then been shackled by the Stormers' defensive line speed, to cut lose but it was the visitors who scored next.
Juarno Augustus had only been on as a replacement back for four minutes when fullback Damian Willemse set him free for the line with a well-timed pass.
Five minutes later and hulking Springboks centre Damian de Allende brushed off a series of tackles to cross after some good work from Leyds and when winger Nel benefited from a Quade Cooper spill to add a third, the score was 31-10.
The Australian Conference leaders still had 24 minutes to save the game but the Stormers continued to tackle as if their lives depended on it and it was not until the 68th minute that scrumhalf Will Genia got their first points of the second half.
A fine run from Marika Koroibete created an opportunity for Campbell Magnay to score another try for the Rebels but it was too late and Nel raced away in the final seconds for his second five-pointer to seal the victory.
(Reporting by Nick Mulvenney in Sydney, editing by Christian Radnedge)
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