Farfus posted the fasted lap for the third consecutive session, beating the German by four hundreths of a second.
Mueller clocked the first significant time with a lap of 2:32.830 on his first attempt but ten minutes into the session, Tom Coronel caused a red flag after leaving half of his SEAT Leon against the barriers at the Mandarin bend.
Moments after the session was resumed Franz Engstler – who had set the Independents pace in the first practice – spun at Moorish Hill while Farfus brushed the barrier at the Lisboa bend.
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Mueller's lap was eventually beaten by Farfus who completed a lap in 2:32.786 with one minute left.
All the four manufacturers – BMW, Chevrolet, Honda and SEAT – were represented in the top seven and only three tenths separated Farfus from Yvan Muller and Robert Huff, sixth and seventh fastest respectively with the same time of 2:33.111.
Championship contender Gabriele Tarquini was down in 12th, 1.3 seconds off the pace.
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