Australian Jess Fox picked up 4 seconds in penalties, which put her 2.52 seconds behind Vilarrubla, with Austria's Nadine Weratschnig third, but Fox comfortably wrapped up the overall World Cup crown.
Slovenia's Peter Kauzer posted one of the closest wins of the season in the men's K1, his time of 86.96 a mere 0.04 seconds ahead of France's Boris Neveu in the men's K1 at the La Seu d'Urgell course.
Czech Vit Prindis finished sixth in the final, enough to secure him the overall 2017 K1 title.
Jones and her fellow New Zealand paddlers will now head to France to prepare for the world championships later this month.