Citroen's reigning WTCC champion set the fastest time in both practice sessions on Saturday morning.
Muller recorded a quickest time of 2m08.066s in practice one, before improving to 2m07.953s in the second half-hour session.
The Frenchman's efforts remained one second slower than Citroen team-mate Jose Maria Lopez's Friday time, which was achieved on new tyres.
Given his struggles at the preceding meeting at Shanghai, Gianni Morbidelli was a surprise second-fastest in Munnich's Chevrolet.
The Hungaroring winner briefly moved to the top of the timing screens thanks to a time of 2m08.243s five minutes before the practice two chequered flag.
Morbidelli's glory was shortlived, as Muller displaced the Italian less than a minute later.
Friday pacesetter Lopez was Muller's closest rival in practice one, ahead of factory Honda pair Gabriele Tarquini and Tiago Monteiro.
In the third C-Elysee, Sebastien Loeb had to be content with sixth spot in the first session, behind compatriot Hugo Valente who was quickest of the RML Chevrolets.
Loeb improved by almost a second later on to take third place, ahead of Monteiro, Lopez and Tarquini.
Citroen is only running three cars this weekend, but Chinese racer Ma Qing Hua will return to the team for the final round in Macau.
Norbert Michelisz improved from 13th on Friday to take seventh in practice one, but fellow Civic WTCC privateer Mehdi Bennani's troubled start to the weekend continued.
The Moroccan failed to complete a flying lap on Friday after experiencing turbo trouble, and only managed to set a time in the final minute of first practice after encountering splitter problems. Bennani ran well wide onto the 130R corner's run-off area on his way to 16th.
Beijing winner Tom Chilton finished just ahead of his ROAL team-mate and experienced Suzuka racer Tom Coronel.
Dutchman Coronel is a Japanese Formula 3 and Formula Nippon champion, and won the reversed-grid WTCC race on the Suzuka East short circuit last year.
Campos TC2 driver Henry Kwong had a slight brush with the barriers in the first sector in practice one and was forced to park his car early in free practice two at Spoon Curve.
The Campos team was in the wars early in the second session, as Serbian Dusan Borkovic crashed his Cruze on the exit of the Degner curve.
Hugo Valente later almost repeated his team-mate's error by spinning at the same place, but escaped making contact with anything solid.
The demanding Suzuka Grand Prix circuit is being used by the WTCC for the first time this weekend, and caught out several drivers.
The hard-trying Valente had earlier left the track at Dunlop bend, while among those to run wide at Spoon bend were Mikhail Kozlovskiy, Tarquini, John Filippi and Valente.
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