Charles Leclerc will start Saturday's Sprint race at Imola from second on the grid, having been beaten by Max Verstappen to top spot.
Verstappen put in a 1:27.999 in the early stages of the Q3 session as drivers circulated on the Soft compound tyres, before the session turned into chaos with the red flags being shown for Alfa Romeo's Valtteri Bottas.
With the Finn parking his car at the side of the track, the lengthy stoppage allowed the rain a chance to intensify and, once the action resumed, Leclerc emerged on track behind the obviously dawdling Verstappen.
Even if Leclerc had managed to get out on track ahead of Verstappen, any chance of improving on his lap time disappeared moments later as McLaren's Lando Norris slid off the track and brought out the red flags again.
Viewed by others:
Leclerc rues "tricky" session
A disappointed Leclerc could be heard on team radio saying that he believed he "had the pace" to take pole position, but put a brave face on as he spoke to media after returning to the pits.
"It was very tricky, especially on the slicks," he explained.
"There were quite a lot of wet patches, so it was all about putting the laps in and waiting for Q3 to put everything together.
"But this is why it's even more frustrating for me because, when it counted in Q3, I did the wrong choice. But it's life.
"We'll learn from it and, at the end, P2 is not a disaster. Everything is to play for tomorrow and after tomorrow, and we'll give it everything."
While Verstappen has taken the official pole position for the Emilia Romagna Grand Prix weekend, this doesn't necessarily mean he'll start from the front when the lights go out to start the main race.
That is due to Saturday's Sprint race determining the starting grid order for Sunday's Grand Prix.
F1 Podcast: Can fast but fragile Red Bull respond to Leclerc's charge?
RacingNews365.com F1 journalists Dieter Rencken, Mike Seymour and Thomas Maher look back over the Australian Grand Prix, where Ferrari's Charles Leclerc triumphed and Red Bull's Max Verstappen retired.