Marquez put it down to "bad luck" but Pedrosa complained that his opponent had broken his bike's sensor for traction control and said it had caused his early finish.
Under new rules introduced this season, MotoGP hands out penalty points for on-track transgressions, with riders who accumulate four points being put at the back of the grid for their next race.
Seven points means a start from pit-lane, while 10 incurs a ban from the next race.
MotoGP weighed the Aragon crash at a 'Race Direction' hearing at Malaysia's Sepang circuit on Thursday with Marquez, Pedrosa and Honda team members present.
"A touch from (Marquez's) left arm broke the rear wheel speed sensor cable on the back of Pedrosa's bike, resulting in a loss of his traction control for the latter which saw him crashing out of the race," it said on its website (www.motogp.com).
Marquez has now accumulated three penalty points after incurring two during a warm-up at Silverstone when he was deemed to have ignored yellow flags from another rider's spill.
On 278 points with four stops left, Marquez leads the title race by 39 points from reigning champion Jorge Lorenzo heading into the Malaysian MotoGP.
Having lost 25 points from Aragon, Honda now leads Yamaha by only a point in the constructors' championship.
(Reporting by Ian Ransom; Editing by Peter Rutherford)
