The Aprilia rider clocked a blistering lap in qualifying earlier in the day after already lowering the circuit record on Friday, finishing 0.089 seconds clear of seven-time MotoGP champion Marc Marquez of Ducati.
Alex Marquez, on his Gresini Ducati, was 0.299 seconds back and will start Sunday's main race in third.
The pole was the 12th of Bezzecchi's MotoGP career and came at a circuit that has long been a happy hunting ground for defending world champion Marc Marquez, who has won seven of the 11 premier-class races held at Aragon.
"We start in a good place, but Marc and Alex are both super fast in terms of pace. It's going to be a tough fight," said Bezzecchi.
"Now the real job starts."
Marc Marquez has won three of the past five races to haul himself back into title contention, but he admitted Bezzecchi was simply too quick in qualifying.
"Sometimes you cannot do anything. You just try to do your best," he said.
The 33-year-old Spaniard then showed his best later in the sprint race, finishing 1.140 seconds ahead of his younger sibling, with Bezzecchi rounding out the podium.
Bezzecchi and the elder Marquez are attempting to close the gap on championship leader Jorge Martin. The Spaniard, riding for Aprilia, could only place fifth in both qualifying and the sprint race.