The Italian, Tarquini, had set the benchmark with a very fast opening lap and his initial effort looked set to be enough to earn him top spot.
But the Chevrolet team managed to enable Menu to roar in front on the timesheets with just seconds left of the session.
Tarquini and the Lukoil Racing Team knew that something special was required late on, but just when the SEAT was ready to leave the pit lane, it was too late for a final flying lap.
Menu said: “I was not happy with my second lap in Q1, as I have made mistakes in a couple of turns. We changed the car a bit for Q2 and my first lap was already a good one, but Gabriele (Tarquini) was able to be even faster.
“I was not sure I could improve, but I prepared for a second attempt. And that lap was perfect.
“The car was fantastic and I did not make mistakes, which was the key on this track.”
Yvan Muller and Rob Huff managed to improve, but were not able to beat Tarquini’s time and qualified in second and third, respectively, ahead of both Norbert Michelisz and Alex MacDowall.
Tom Coronel spoiled his Q1 by spinning on new tyres, while Pepe Oriola could not make any better that 18th.
Team Aon drivers James Nash and Tom Chilton were not able to repeat the encouraging results they enjoyed in practice.
Mehdi Bennani and Stefano D’Aste qualified in ninth and 10th, meaning a full BMW front row on the reversed grid.