In Q2, Magnussen hit the wall coming out of Speaker's Corner and, with his damaged Haas, the Dane stuck to the racing line through the following corners, severely hindering Leclerc.
The Monegasque driver made his displeasure known on the team radio and called for Magnussen to be penalised.
Following a post-session investigation, the stewards slapped Magnussen with a three-place grid penalty for Sunday's race, as they said that he and his Haas team should have taken more care to avoid holding up the Ferrari.
In their verdict, the stewards wrote: "Magnussen left the track at Turn 9 and made contact with the wall. He then rejoined and drove the dry line.
"Leclerc, who was on a fast lap, caught Magnussen who did not give way until Turn 16.
"Magnussen explained that he did not feel it was safe to move off onto the wet at speed and give room to Leclerc, particularly in the turns between 11 and 15.
"The Stewards observed that he did not receive a warning from his team that Leclerc was behind until Leclerc was right behind him at Turn 10. The team also told him to push, as he needed to make it to the line to get another lap.
"Whether it was his failure to slow and yield following his accident, or whether it was the team's failure to give information early enough that he could have pulled off earlier, or whether it was the instruction to push through the lap; in any case the Stewards determine that he unnecessarily impeded Leclerc."
The penalty drops Magnussen from 13th to 16th on the grid, as the damage sustained in the contact with the wall damaged his car too much to improve on his final lap and advance to Q3.
"I hit the wall in Turn 9 exit and damaged the car, the rear wing and the floor, so got another attempt, but obviously but it was with the damaged car," Magnussen said when asked about his off by Motorsport.com.
"I think I made the best of it but shouldn't have been off, of course. The car was pretty damaged, I was in the tyre wall."
After cooling down and reviewing the incident, polesitter Leclerc showed more understanding of the difficult situation Magnussen was in.
"There's just one dry line, it's very difficult to go outside of the dry line on slicks," he conceded.
"In normal circumstances, you would have moved away from the racing line, but in those conditions, it's not that easy."
Additional reporting by Adam Cooper
