It had been Auer that held the lead heading into the final five minutes, ahead of BMW’s practice pacesetter Augusto Farfus, before Juncadella leapt to the head of the order with less than a minute left on the clock.
Auer improved thereafter but not by enough to beat the Spaniard, while reigning champion Rene Rast’s final lap was good enough to put him third, a further tenth behind in the best of the Audis.
Philipp Eng led the BMW charge in fourth, just 0.002s behind Rast, while Farfus slipped to fifth in the closing stages.
Points leader Gary Paffett suffered an off at Paddock Hill in the first part of the session, glancing the barrier, but the Mercedes driver avoided major damage and was able to set the sixth-fastest time when he returned to the track.
Ex-Formula 1 driver Timo Glock spun off at Surtees at the very end of the session, bringing out the yellow flags, but had set a time good enough for seventh.
Edoardo Mortara (Mercedes), Marco Wittmann (BMW) and Pascal Wehrlein (Mercedes) completed the top 10.
Rast was the only Audi driver to breach the top 10, with the Ingolstadt marque’s next-best placed representative being Robin Frijns in 11th place.
Jamie Green’s struggles continued at his home track, the series veteran qualifying on the back row alongside BMW man Bruno Spengler.