Muller led from lights to flag and was followed home by a trio of his SEAT Sport team-mates in Jordi Gene, Rickard Rydell and Gabriele Tarquini.
Nicola Larini crossed the line fifth in the new Chevrolet Cruze but was demoted after the stewards decided to give him a 30-second penalty for overtaking Augusto Farfus at the restart following a safety car period.
Farfus and Sergio Hernandez were the best of the BMW men. They were promoted to fifth and sixth ahead of Larini.
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Felix Porteiro won the Independents' class in eighth position and claimed pole for race two after Tiago Monteiro suffered the same penalty as Farfus.
A pile up at turn four on the first lap eliminated three of the major contenders in Joerg Mueller, Britain's Andy Priaulx and Alain Menu.
Mueller swerved to the left, hit Priaulx and spun collecting Menu. The latter retired while Mueller pitted for repairs and rejoined five laps later.
Priaulx rejoined immediately and recovered from 21st to finish ninth.
The race was further disrupted by the safety car from lap six to nine after Stefano D'Aste crashed at the Esse de Alta.
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