Perez was on a warm-up lap for his first Q1 run when a hotlapping Hulkenberg encountered him in the middle of the racing in on Turn 13, Albert Park's slow penultimate left-hander.
The Mexican was only told very late by his race engineer that the Haas driver was behind him, with the focus instead being on preparing his flying lap.
Perez was summoned by the stewards after qualifying, in which he took third place behind Red Bull team-mate Max Verstappen and Ferrari's Carlos Sainz.
The stewards handed him a three-place grid drop, instead demoting him to sixth on Sunday's starting grid.
"Hulkenberg was on a fast lap when he approached turn 13," their verdict said.
"Perez, who was on an out lap was at the apex of the turn and Hulkenberg had to leave the racing line to drive around him. Hulkenberg was forced to lift the throttle early and brake early for that corner.
Source: Autosport