In Q1 Piastri blocked Haas driver Magnussen into the Tamburello complex on the Dane's final flyer.
The incident ruined Magnussen's session, going out in 18th while team-mate Nico Hulkenberg advanced to Q3.
Piastri said that he "didn't see any cars coming" in his mirror because the main straight before Turn 2 curves to the left, leaving Magnussen in his blind spot.
While the FIA race stewards sympathised with the Australian, they judged it was the duty of the team to warn its driver of approaching traffic before it was too late, which they explained happened correctly in all other instances on Saturday.
They wrote: "In fact there was an approximately 140km/h speed differential and Magnussen was only approximately 40-50m behind at the time and this meant that Piastri was in the middle of the chicane when Magnussen caught up directly behind Piastri.
"Further, it was clear that Magnussen was on a fast lap since his exit of Turn 19.
"Traffic management for slower cars is an extremely important part of the team/driver combination, particularly in Q1. In this instance the stewards determine that the lack of sufficient warning caused an "unnecessary impeding."
The three-place grid drop bumps Piastri from second to fifth after qualifying less of a tenth behind polesitter Max Verstappen in Q3.
Team-mate Lando Norris and both Ferraris of Charles Leclerc and Carlos Sainz all move up a spot.
McLaren team boss Andrea Stella said he accepted the decision, acknowledging that the team should have done a better job communicating.
"The assessment and the judgment of the stewards, we respect it," Stella responded.
"We need to improve our operations. We move on and hopefully tomorrow we will recover the positions that we lost today on the grid."
Piastri said he was otherwise buoyed by McLaren confirming its Miami progress in Imola, where he has also received the full upgrade package from the team.
"I've been happy with it all weekend to be honest, from the start of P1 all the way through qualifying," he said.
"Having parts that you know are going to make the car faster on the car is always a confidence boost.
"I think our long runs yesterday looked good, but it's very, very close. I think that's been the story of the season and the last few races, everyone's been so tight.
"Overtaking is very tough here, but I think we can be optimistic."
