It had been Muller who held the advantage in Q1 and again after the first set of flyers in Q2, with his 1m45.708s more than three tenths better than his rivals could manage.
Chilton began his final flyer just before the chequered flag came out however, and an outright best in the first sector helped him to prevail by just over one tenth of a second.
The Briton had in some ways been lucky simply to be out in Q2, having only narrowly avoided contact with the Turn 2 barriers after slewing off track late on in Q1.
Honda will line up on the second row through Tiago Monteiro, who spoiled a Chevrolet top-three lockout by beating Pepe Oriola to third.
Bamboo duo Alex MacDowall and James Nash will share the third row, making it five Chevrolets in the top six.
Norbert Michelisz beat defending champion Rob Huff to seventh, but will start from the back of the grid after an engine change in his Zengo-run Honda.
Muller's closest title rivals, Michel Nykjaer and Gabriele Tarquini, shared the fifth row in qualifying but will both gain one spot following Michelisz's penalty.
Tarquini had to abandon his first Q2 run and also had several lairy moments on his final attempt, but did just enough to edge out Mehdi Bennani and Marc Basseng in the fight for 10th, and with it race two's reverse-grid pole.
Bennani and Basseng had both secured their Q2 spots in the final moments, bumping BMW men Tom Coronel and Freddy Barth out.
The latter pair both missed out by less than one tenth of a second, with Coronel ruing traffic that spoiled his best lap and left him with a "disaster" of a grid position.
James Thompson was Lada's best representative in 18th. He missed the Q2 cut by six tenths of a second.
Pos Driver Team/Car Time Gap
1. Tom Chilton RML Chevrolet 1m45.583s
2. Yvan Muller RML Chevrolet 1m45.708s +0.125s
3. Tiago Monteiro Honda 1m46.240s +0.657s
4. Pepe Oriola Tuenti Chevrolet 1m46.266s +0.683s
5. Alex MacDowall Bamboo Chevrolet 1m46.411s +0.828s
6. James Nash Bamboo Chevrolet 1m46.565s +0.982s
7. Norbert Michelisz Zengo Honda 1m46.648s +1.065s
8. Rob Huff Munnich SEAT 1m46.659s +1.076s
9. Michel Nykjaer Nika Chevrolet 1m46.668s +1.085s
10. Gabriele Tarquini Honda 1m46.865s +1.282s
11. Mehdi Bennani Proteam BMW 1m46.919s +1.336s
12. Marc Basseng Munnich SEAT 1m47.711s +2.128s
13. Tom Coronel ROAL BMW 1m47.038s Q1
14. Fredy Barth Wiechers BMW 1m47.078s Q1
15. Darryl O'Young ROAL BMW 1m47.126s Q1
16. Hugo Valente Campos SEAT 1m47.145s Q1
17. Franz Engstler Engstler BMW 1m47.277s Q1
18. James Thompson Lada 1m47.583s Q1
19. Stefano D'Aste PB BMW 1m47.637s Q1
20. Charles Ng Engstler BMW 1m47.892s Q1
21. Fernando Monje Campos SEAT 1m48.025s Q1
22. Mikhail Kozlovskiy Lada 1m48.070s Q1
23. Rene Munnich Munnich SEAT 1m48.279s Q1
24. Tom Boardman Special Tuning SEAT 1m48.530s Q1
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