The GP3 race winner timed his flying laps perfectly as isolated rain showers became heavier towards the halfway point in the half-hour session, rendering his early fastest lap of 1m42.174s unbeatable.
Palou, who is racing for the Teo Martin squad this weekend in place of Nelson Mason, was more than half a second clear of championship leader Pietro Fittipaldi - whose 1m42.841s put him at the head of a six-car chain separated by just 0.326 seconds.
Third place went to Matevos Isaakyan, who was the only driver other than Palou and Fittipaldi to dip below the 1m43s barrier as he edged out Force India junior Alfonso Celis by two-hundredths of a second.
Celis spent some time on the provisional front row, but was demoted by a flurry of fast laps from others while himself failing to improve just before the track became soaked.
The battle for fifth and sixth was even closer as Roy Nissany did his title chances no harm by outqualifying Aragon race winner Egor Orudzhev by 0.001s.
Rene Binder will have to work hard to maintain his second place in the championship as he could only qualify in 10th - the best part of one second slower than Lotus team-mate Fittipaldi and 1.4s off pole.
Ahead of him, Fortec Motorsport driver Diego Menchaca could not replicate the pace he showed in morning practice and will start eighth alongside Konstantin Tereschenko on the fourth row.
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