The home team, who had lost 35-8 in Cape Town in March, scored an early try when a neat dummy by flyhalf Domingo Miotti let fullback Emiliano Boffelli dart through a gap to pass to flanker Pablo Matera, who touched down under the posts.
Jaguares indiscipline allowed the Stormers to keep in touch throughout and the visitors kicked six penalties -- four by flyhalf Jean-Luc du Plessis and two by fullback Damian Willemse.
Matias Orlando, Jaguares captain for the day in the absence of injured fellow centre Jeronimo de la Fuente, said the win had come despite his side making lots of mistakes and wrong decisions.
"We got three nice tries that show that when we do things right and are efficient and believe in ourselves, things work out. But we've got to do a lot of thinking about the rest of the match," he added.
"They kept adding in threes because of avoidable errors on our part and for that reason they were in the match to the end."
Miotti had the home side 13-9 ahead at halftime with his second penalty but a fourth from du Plessis right after the interval kept the Stormers on their heels.
Wing Ramiro Moyano scored the Jaguares’ second try and the Argentine team were awarded a penalty try 10 minutes from time for a deliberate knock-on by JJ Engelbrecht, who was sent to the sin bin.
A late try by replacement wing Seabelo Senatla gave the Stormers a chance to snatch victory in the final minutes, but with the Jaguares down a man with Matera sin-binned the visitors fluffed a throw-in and failed to capitalise.
The win moved the Jaguares three points ahead of the Stormers in the South African conference, and within a point of the Bulls and Sharks.
(Editing by Peter Rutherford)
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