The German had posted a time good enough to join Max Verstappen on the front row of the grid in Q3, seconds before the red flag was issued by the stewards following Oscar Piastri's crash on the exit of Turn 7.
Following the clean-up operation of the Australian's stranded McLaren, the session resumed but in far worse conditions than those that had preceded the short hiatus.
This cemented Hulkenberg's provisional position on the front row, as Fernando Alonso was unable to complete his time as he was in contention to join Verstappen on the front row.
According to a document circulated by the FIA after the conclusion of the session, Hulkenberg had earned a summon to the stewards' room for an "alleged breach of Article 37.6 a) of the FIA Formula One Sporting Regulations - Car 27 failing to stay above the minimum time set by the FIA ECU at 16:59."
There is a minimum time required for the drivers to return to the pitlane following a red flag, but radio messages between Hulkenberg and race engineer Gary Gannon suggested that he was going too quickly to meet the required delta, which has warranted an investigation.
The Haas driver narrowly escaped elimination in Q1 as AlphaTauri's Yuki Tsunoda was unable to set a time good enough to dump Hulkenberg into the danger zone at the end of the session.
Haas also joined the slick-tyre running in Q2 with enough time before the rain return to allow Hulkenberg to earn safe passage into Q3, at the expense of Ferrari's Charles Leclerc.
As conditions worsened in time for Q3, Hulkenberg managed to get enough temperature into his intermediate tyres to ensure he could set a 1m27.102s on his second tour of the circuit, nudging Alonso out of the top two.
The red flag emerged as Hulkenberg reached Turn 2 on his cooldown lap, with race engineer Gary Gannon telling him to ensure that he was "plus on delta time".
Hulkenberg then reported that the "beeping [in his ear] is going nuts here, do I need to be negative or positive?", with Gannon telling him to slow down, but amid confusion between the two, Hulkenberg felt that he was going too slow having just passed Piastri's crashed car.
Gannon then told him to change engine modes, with Hulkenberg following up by asking "is this too fast or too slow?" - the reply coming that he needed to slow down as he exited the hairpin prior to pitting.