Muller came through from ninth on the grid to finish fourth, right on the tail of Norbert Michelisz's Zengo Honda. Poleman Mehdi Bennani was second.
As was the case in the opening contest, the order at the front was set away from the line, with Tarquini managing to stick it out around the outside of Bennani at Turn 1 and therefore slip by on the inside of Turn 2.
Bennani settled into second, but soon came under increasing pressure from Michelisz, who set the fastest lap of the race in a bid to close an early deficit.
Michelisz's attack turned to defence however as Muller picked off Tiago Monteiro, James Nash and Rob Huff - the latter of whom suffered a puncture while running third - in quick succession and began to close on the frontrunners.
With one lap to run Muller was all over Michelisz's rear, but despite his best efforts the Hungarian held on to clinch the final spot on the podium.
Monteiro never let Muller get away and finished just three tenths down the road in fifth.
Tom Coronel came through from 12th to finish a relatively lonely sixth, while Freddy Barth sealed seventh after a late pass on Nash.
The Briton was on the defensive throughout the race, and eventually wound up eighth, with Marc Basseng and Stefano D'Aste both less than one second down the road.
Race one winner Tom Chilton lost ground at the start and could only capture 11th, which only came after a frantic late fight with Darryl O'Young.
Tarquini's victory helped Honda secure this year's manufacturers' title, which it contested exclusively with Lada.
Results - 13 laps:Pos Driver Team/Car Time/Gap
1. Gabriele Tarquini Honda 23m40.401s
2. Mehdi Bennani Proteam BMW +2.434s
3. Norbert Michelisz Zengo Honda +4.099s
4. Yvan Muller RML Chevrolet +4.606s
5. Tiago Monteiro Honda +4.941s
6. Tom Coronel ROAL BMW +7.735s
7. Fredy Barth Wiechers BMW +14.165s
8. James Nash Bamboo Chevrolet +17.865s
9. Marc Basseng Munnich SEAT +18.746s
10. Stefano D'Aste PB BMW +19.234s
11. Tom Chilton RML Chevrolet +20.858s
12. Darryl O'Young ROAL BMW +22.239s
13. Alex MacDowall Bamboo Chevrolet +24.265s
14. Hugo Valente Campos SEAT +24.436s
15. Fernando Monje Campos SEAT +31.098s
16. James Thompson Lada +32.650s
17. Michel Nykjaer Nika Chevrolet +32.794s
18. Mikhail Kozlovskiy Lada +47.352s
19. Rene Munnich Munnich SEAT +47.553s
20. Rob Huff Munnich SEAT +1 lap
Pepe Oriola Tuenti Chevrolet 10 laps
Tom Boardman Special Tuning SEAT 9 laps
Charles Ng Engstler BMW 6 laps
Franz Engstler Engstler BMW 2 laps
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