The Pramac Ducati rider opted for slicks on a drying track while most of the big names decided to stay on wet weather tires, and seized the top slot in the dying seconds at the Termas de Rio Hondo circuit.
Miller, who did two qualifying laps on wets before returning to the pits and asking for slicks, was the first independent Ducati rider to take a pole position in the top-flight.
“It wasn’t me. I was just hanging on,” said the Australian of his performance.
“I was a passenger. When you’re on wet with slick tires... you’ve just got to hang on and hope to God you make it to the other side.”
Honda’s Spanish veteran Dani Pedrosa was second fastest, 0.177 slower than Miller’s time of one minute 47.153 seconds, with Frenchman Johann Zarco a close third for the non-works Tech3 Yamaha team.
Reigning champion Marc Marquez, Pedrosa’s team mate and the race favorite, will start in sixth place while Ducati’s championship leader Andrea Dovizioso qualified eighth.
“I decided to try the slick tires but it was too risky,” said Marquez. “As soon as I exited the pit I realized that if I touched the wet side of the track the risk of crashing was great.
“It’s a pity we’re not on the front row but I’m happy because I think we’ve worked well this weekend.”
