The Spaniard started on pole at the first race at the Circuito de Jerez in the history of the series and won his duel with compatriot Mikel Azcona to end the campaign in style.
Azcona went on to claim victory in the second race of the weekend but it was too little too late.
It is Nogues' second European crown, following on from 2012, after being discovered in 1999 by a talent search campaigned by Renault Catalonia.
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In race two, Azcona started on pole and took the chequered flag despite pressure throughout from Nogues.
The win for Azcona saw him finish the season in the runner-up position behind his fellow Spaniard, with France’s Eric Trémoulet, who finished third for the second time over the weekend, bumped down to third overall.
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