Palou, who is replacing Nelson Mason at Teo Martin Motorsport for the third consecutive round, set his 1m49.411s with less than two minutes of the session remaining.
Struggling to find a set-up that suited him during Thursday's practice sessions, he found the right balance in the car for first qualifying - where he finished fourth - and made minor tweaks for race two qualifying.
Joining him at the front is championship leader Pietro Fittipaldi. The Lotus driver set exactly the same time as Palou, but as his lap was set as the chequered flag came out he couldn't snatch pole position away.
Egor Orudzhev, also a championship contender, finished just one-tenth away from pole with a 1m49.535s.
Throughout the session the SMP Racing driver regularly set front-running times but couldn't find extra time when it mattered.
He'll be joined on row two by race one polesitter Rene Binder, who struggled to live with the extra pace of the trio in front and left it until his last lap to claim fourth place.
It was a brace of fifth places for Matevos Isaakyan as the Russian, who is second in the championship standings, couldn't break into the 1m49s with a 1m50.081s.
Alfonso Celis will line-up on the third row with his final lap of the 30-minute session relegating Roy Nissany to seventh by 0.008s.
Diego Menchaca will provisionally start eighth but was told to report to the stewards after qualifying because of a pitlane speed violation.
Rounding out the field is Konstantin Tereschenko, Yu Kanamaru and Giuseppe Cipriani.
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