It had appeared that Dani Pedrosa had negotiated the changing conditions at the Termas de Rio Hondo best, with the Spaniard top when the chequered flag was waved.
But Australian Miller came out of nowhere to post a time of one minute and 47.153 seconds to ensure he will head the grid on race day.
Pedrosa and Johann Zarco – who was on pole for the MotoGP season-opener in Qatar – complete the front row.
Marc Marquez had finished top of FP2, 3 and 4, but the Spaniard struggled on the slicks on a drying track, and opted to revert to the wet bike.
However, the world champion could only qualify sixth, behind Tito Rabat and Alex Rins, who were fourth and fifth.
Provisional Classification:
Jack Miller (Ducati Pramac): 1:47.153secs
Dani Pedrosa (Repsol Honda): 1:47.330s
Johann Zarco (Monster Yamaha): 1:47.365s
Tito Rabat (Reale Avintia Racing): 1:47.681s
Alex Rins (Suzuki Ecstar): 1:47.743s
Marc Marquez (Repsol Honda): 1:47.754s
Aleix Espargaro (Aprilia): 1:47.845s
Andrea Dovizioso (Ducati): 1:48.247s
Maverick Vinales (Movistar Yamaha): 1:49.044s
Cal Crutchlow (LCR Honda): 1:49.304s
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