Lorenzo's Yamaha team-mate Ben Spies continued his shocking season by crashing out on lap nine and Andrea Dovizioso also then crashed out of fourth position at turn seven. He was able to rejoin.
Pedrosa edged ahead of Lorenzo at the end of lap 10 before Crutchlow and then Stefan Bradl both crashed out in quick succession as the conditions deteriorated. Crutchlow has now failed to finish in four of his last six races.
Lorenzo signalled for the race to be stopped, before he almost crashed out with six laps to go. The race was then red flagged.
MotoGP: Sandro Cortese wins Moto3 championship
race, Cortese needed to finish in the top three to take the title after his main rival Maverick Vinales surprisingly
quit his Blusens team on Friday,
calling them a "second division" outfit.
The race started in 35C heat but spots of rain began to fall over some of the circuit with nine laps to go.
Malaysian rider Zulfahmi Khairuddin led for most of the race but Cortese was able to pass him on the final lap to win and seal the inaugural Moto3 crown in style.
Cortese, 22, said: "I can't believe it. It is a dream come true."
The rain then arrived in force, with a downpour delaying the start of the
race by half an hour.
Championship leader Marc Marquez was shifted down the standings early on as British rider Rea briefly led.
Marquez then crashed out with seven laps remaining as the rain returned and the race was red flagged as the conditions detoriated.
Alex De Angelis was awarded the win, with Anthony West in second and Rea in third.
Malaysian MotoGP results (Standings after 13 laps):
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