Di Resta failed to improve on his second set of runs, securing Paffett a fourth pole of the season.
Former Manor and Sauber Formula 1 driver Pascal Wehrlein completed the top three, qualifying only 13 thousandths slower than di Resta.
Rene Rast was the fastest non-Mercedes driver in fourth, a little more than a tenth off the pace in his Audi RS5, ahead of Saturday front row starter Lucas Auer and Robin Frijns.
Race one runner-up Augusto Farfus was BMW’s leading representative in seventh, with Loic Duval (Audi) eighth ahead of another two BMW drivers – Marco Wittmann and Philipp Eng.
The third Briton on the grid, Jamie Green, was 11th and less than four tenths off pole in his RS5 ahead of Mike Rockenfeller.
All but one of the 18 cars qualified within a second of each other, with Bruno Spengler bringing up the rear by improving to a 1m19.115s on his final lap.