Honda rider Marquez holds a 39-point lead over reigning champion Jorge Lorenzo with four rounds of the season remaining.
Marquez had briefly faced the threat of a grid penalty for this weekend's race at Sepang after he was called to a Race Direction hearing on Thursday following his clash with team-mate Dani Pedrosa in the previous race at Aragon.
But it was confirmed on the MotoGP website that the 20-year-old had had a single penalty point added to his season total.
Marquez had previously accrued two penalty points, but a tally of four is needed for a rider to be put to the back of the grid for the next race.
"We are sending a message to Marc, very clearly, that we understand that he is an extremely talented rider but he is also intelligent enough to understand that there has to be some margin for error," MotoGP race director Mike Webb told the series website.
"For us [the Aragon crash] is a signal (even though the contact itself was quite minor) to make a formal warning by way of a penalty point to Marc to say he has to take more care."
Honda also lost the 25 points they gained in the constructors' championship from Marquez's win as a result of the traction control failure - caused by contact between the two team-mates - that saw Pedrosa crash out in Aragon.
It leaves them just one point clear of Yamaha at the top of the standings.
Yamaha rider Lorenzo admits he faces a difficult task to stop Marquez claiming the crown, the youngster having made the most of injuries suffered by the two-time champion and Pedrosa during the middle section of the season, while escaping relatively unscathed from several big crashes of his own.
Lorenzo, returning to the track where he won his first title in 2010, said: "I have some good memories here but we need to keep focus now on the race and try to recover a little bit to Marquez. The championship is difficult but we want to fight until the end. Let's see what happens."