The Haas driver was found to have gone faster than the minimum delta time set by the FIA ECU on his return to the pits when the session was red flagged in Q3, as Oscar Piastri put his McLaren in the wall at Turn 7 amid wet conditions in Montreal.
Hulkenberg had set a lap good enough for second on the grid moments before the red flag emerged, and the worsening rainfall ensured that nobody was able to improve when the session restarted.
The session was stopped as Hulkenberg hit the opening pair of corners, and as a result he was 1.5 seconds over the delta time which he was unable to rectify.
The penalty thus moves him back to fifth on the grid, as Fernando Alonso will now join Max Verstappen on the front row.
In the official documentation supplied by the stewards, the FIA noted: "The driver had just finished his fastest lap and had started another push lap. He was at T1 when the red flag was displayed, however at that point he was already 1.5 seconds over his delta time.
"He claimed this made it extremely difficult for him to come below the delta in the next sector. He also admitted to confusion about the beep signal in his headset, and therefore at one stage thought he was going too slow.
"Comparison of telemetry with that of Car 31 showed that in general for the rest of the lap he was approximately the same speed as Car 31 which complied with the delta times in each mini-sector. We regard this as a mitigating circumstance.
"However, the regulation is very clear and whilst there is no question of the driver acting dangerously or driving unsafely, there was a breach and thus a penalty has to be imposed. The normal penalty for failure to slow under red flags is 10 grid positions, however in view of the mitigating circumstance, a lower penalty is appropriate.
"We note the intention of the regulation is to ensure a car is not speeding during a red flag situation and there is no evidence that the speed was excessive in this case. We also note that the driver should make himself more familiar with the operational aspects of the delta signals."
Radio traffic between Hulkenberg and race engineer Gary Gannon unveiled confusion between the two over the delta time.
Here's the full radio transcript between the two:
Gannon: Red flag, red flag. Need to be plus on delta time, plus on delta time.
Gannon: Okay, that time counted - very good lap, currently P2.
Gannon: Okay so, Piastri - go to mode "slow", just charge on. Piastri crashed on the exit of T7, Piastri is on the left, exit of seven so watch for Piastri.
Hulkenberg: The beeping is going nuts here, should I be negative or positive?
Gannon: You should be positive now. Plus, so you need to slow down. Slow down, and it's a double waved yellow here, watch for Piastri here, this is where Piastri crashed.
Hulkenberg: I think I'm going too slow, I think I need to be faster.
Gannon: Okay, I've just checked with Mike -
Hulkenberg: - you tell me.
Gannon: Get out of this mode, press "in".
Hulkenberg: Is this too fast or too slow?
Gannon: It's too fast, slow down, because it's a red flag.
Gannon: Okay so we'll box now, Nico, box now.
There was precedent for the penalty as Daniel Ricciardo received a penalty to the same magnitude in qualifying for the Australian Grand Prix back in 2018, having failed to slow sufficiently during a red flag for debris on the circuit.
In further penalty news, Lance Stroll received a three-place grid drop for impeding Esteban Ocon in Q2, while Yuki Tsunoda was cleared of impeding Charles Leclerc - but also collected a three-place penalty for blocking Hulkenberg during Q1.
Hulkenberg progressed into Q2 at the expense of Tsunoda, as the Japanese driver could not improve on his final lap.
Carlos Sainz also picked up a three-place grid drop for impeding Pierre Gasly.