The late slip up means the four-time MotoGP championship winner will line up for the first qualifying session for only the fourth time in his career, reports Efe news.
Italian Andrea Dovizioso (Ducati) was fastest during final practice, posting a 1:30.399s with just two minutes left in the session.
Australia’s Jack Miller (Pramac) was second quickest, notching a 1:30.566, with Spaniard Maverick Vinales following in third.
Sunday’s race will not feature Spain’s Jorge Lorenzo, who suffered a hairline fracture to left wrist after a dramatic crash during practice on Friday.
The Thailand MotoGP Grand Prix will take place on Sunday.