The Alsace driver set a stunning first sector time en route to a pole time of 1m48.727s.
Championship leader and Q1 pacesetter Jose Maria Lopez finished just 0.034 seconds adrift in second, while former World Rally Championship king Sebastien Loeb completed a Citroen lock-out of the top three.
"I am pleased to open my real pole account for the season," said Muller.
The meeting is the first occasion where Citroen has carried 60kg of compensation weight. Muller stated that simulations had shown a 0.8s per lap penalty because of the weight.
Honda produced a much improved showing in Hungary over its early season efforts. Gabriele Tarquini's final Q2 lap secured the Italian top billing on the timing screens, and factory JAS team-mate Tiago Monteiro appeared competitive in third.
Tarquini's performance could not be maintained in the decisive Q3 session for the five fastest Q2 runners, where he was over a second slower than his Q2 effort after a scruffy lap. He finished behind Monteiro in fifth.
Customer Honda runner Mehdi Bennani threatened to cause an upset by bumping Loeb from Q3. The Moroccan Proteam driver had to settle for a still impressive sixth in Q2, ahead of leading Chevrolet driver Tom Chilton.
Reigate driver Chilton, who headed a gaggle of five RML-built Cruzes in the second segment of qualifying, was partnered by ROAL team-mate Tom Coronel for the first time since the Marrakech season opener.
Dutchman Coronel was ruled out of round two in France owing to a heavy crash in Morocco, but personnel at ROAL and RML worked long hours to ready a new car for the WTCC veteran in time for Hungary.
After a shock absorber problem on Friday, Coronel finished behind Chilton in eighth.
Provisional 10th-place qualifier Dusan Borkovic's Q1 and Q2 times were cancelled after his Campos Chevrolet failed a ground clearance check, moving his team-mate Hugo Valente both up a position and onto reversed-grid pole.
On the circuit where he scored his lone Formula Renault 3.5 win, series returnee Pasquale di Sabatino took the TC2 pole honours for Engstler Motorsport.
Pos Driver Team/Car Time Gap
1. Yvan Muller Citroen 1m48.727s
2. Jose Maria Lopez Citroen 1m48.761s +0.034s
3. Sebastien Loeb Citroen 1m49.113s +0.386s
4. Tiago Monteiro Honda 1m49.166s +0.439s
5. Gabriele Tarquini Honda 1m50.576s +1.849s
6. Mehdi Bennani Proteam Honda 1m49.745s Q2
7. Tom Chilton ROAL Chevrolet 1m49.757s Q2
8. Tom Coronel ROAL Chevrolet 1m50.428s Q2
9. Gianni Morbidelli Munnich Chevrolet 1m50.728s Q2
10. Dusan Borkovic Campos Chevrolet 1m51.937s Q2**
11. Hugo Valente Campos Chevrolet 1m52.123s Q2
12. Norbert Michelisz Zengo Honda Q2
13. Rob Huff Lada 1m50.908s Q1
14. James Thompson Lada 1m50.995s Q1
15. Rene Munnich Munnich Chevrolet 1m51.123s Q1
16. Mikhail Kozlovskiy Lada 1m52.451s Q1
17. Pasquale di Sabatino Engstler BMW 1m54.584s Q1*
18. Franz Engstler Engstler BMW 1m55.121s Q1*
19. Yukinori Taniguchi Nika Honda 1m56.561s Q1*
20. John Filippi Campos SEAT 1m56.588s Q1*
* TC2 ** Later disqualified
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