The Frenchman kept Norbert Michelisz behind at the first braking then controlled his rival throughout the 12 laps of the circuit.
He increased the gap from laps three to six then fended off his charging rival late on.
Behind them Gabriele Tarquini claimed third place, benefiting from the battle for fourth place which involved Rob Huff, Mehdi Bennani, Tom Coronel and Tom Chilton.
Eventually Huff was classified fourth ahead of Bennani who scored his first victory in the Yokohama Trophy.
A pile-up after the start eliminated some potential top players such as Tiago Monteiro, Pepe Oriola, Fredy Barth and James Thompson. Coronel and Darryl O’Young are currently under investigation for this.
Start – Muller sprints from pole to take the lead from Michelisz, Tarquini and Huff
Lap 1 – Coronel hits Monteiro at Turn 2, behind them a pile up eliminates Oriola and Thompson and forces Barth, O’Young and D’Aste to pit for repair
Lap 2 – Monteiro outbrakes himself at Turn 1 and crash into the tyre wall
Lap 2 – Coronel overtakes Bennani for sixth
Lap 5 – Coronel and Bennani overtake Chilton at Turn 13 and move up to fifth and sixth
Lap 6 – Muller and Michelisz pull away, Muller leads by one second
Lap 7 – close fight for third between Tarquini, Huff, Coronel and Bennani
Lap 9 – Huff is put under pressure by Coronel
Lap 10 – Huff and Coronel drive side-to-side, Bennani overtakes Coronel for fifth
Lap 11 – Chilton chases Coronel for sixth
Lap 12 – Michelisz closes in on Muller, but the Frenchman maintains the lead