The decision to bestow just one penalty point means Marquez avoids any form of grid penalty for now.
Under MotoGP's new-for-2013 penalty system, any rider reaching four penalty points is put to the back of the grid for the next race.
Seven penalty points earn a pitlane start while a race ban is imposed for anyone who accumulates 10.
Marquez already had two penalty points for his crash in the Silverstone warm-up, which occurred under yellow flags for Cal Crutchlow's accident shortly beforehand.
The Sepang hearing was called after Pedrosa had a violent fall in the Aragon race following minor contact with Marquez, which broke part of the former's traction control system.
Honda has also lost the 25 constructors' points from Marquez's Aragon win. That reduces its advantage over Yamaha to just one point.