Port Adelaide's Darcy Byrne-Jones was running with the flight of the ball when Pearce cannoned into him from the opposite direction in Fremantle's 49-point win on Saturday night.
Although Pearce didn't turn his body in a bumping motion, he took his eyes off the ball at the last moment and was airborne when contact was made.
Pearce's upper arm made contact with Byrne-Jones's head, and the incident was made worse when the Port forward's head slammed into the turf as he landed.
Byrne-Jones was immediately taken from the field and soon subbed out with concussion.
The incident was assessed as careless conduct, severe impact and high contact, drawing a three-match ban.
Pearce will miss games against Gold Coast, North Melbourne and Essendon unless Fremantle successfully challenge the verdict.
They have until Tuesday morning to decide whether to fight the charge.
After Saturday's match, Fremantle coach Justin Longmuir said Pearce shouldn't have anything to worry about.
"From what I saw, Alex is making a play on the ball," Longmuir said.
"What's Alex supposed to do in that situation? Pull out of that contest and let him mark it, going back with the flight? He'd get crucified.
"If Alex pulled out of that contest, that's what would happen. So I don't have any issues with it."
Longmuir described the collision as "unfortunate contact that happens in our game".
"It happens in marking contests a lot, and I see it as one of those situations," he said.
"I didn't think it was a free kick. I've got no issues with it being paid a free kick, but I didn't really think it was a free kick.
"I just thought it was two guys contesting the ball."
Port Adelaide coach Ken Hinkley acknowledged there was no malice from Pearce, but felt the incident would probably be punished.
"Once upon a time they were footy incidents that weren't such a big issue, but they are now, and rightly so because of the concussion," Hinkley said.
"I'm sure both players went at the ball pretty reasonable, but in the end, there was a brace, seemed like a brace that causes some problems.
"And whether that's Darcy hitting his head on the ground or not, it causes a concussion.
"I'm sure Pearce wouldn't have meant that, but it'll play out with the AFL like it always does."
Sydney captain Callum Mills is also set to be in trouble after launching into the air and collecting Melbourne's Charlie Spargo high in Sunday's match at the MCG.
Mills, playing his first AFL match of the season, jumped and turned his body as he and Spargo competed for a loose ball.
In other MRO news, North duo Jy Simpkin and Nick Larkey were fined for separate striking charges, while their teammate Paul Curtis was fined for rough conduct.
Fremantle pair Andrew Brayshaw and Caleb Serong, as well as star Brisbaner defender Harris Andrews were among other players fined for various incidents.
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