By rights, he should have crashed out of the race and scored zero points.
With title rival Dani Pedrosa clear in the lead, the whole complexion of the title chase could have changed. But instead Lorenzo somehow managed to save the crash, superbly stopping his Yamaha and managing to stay on the track.
Standings with two races left
Jorge Lorenzo: 330 points
Dani Pedrosa: 307 points
Casey Stoner: 213 points
Andrea Dovizioso: 195 points
Alvaro Bautista: 154 points
Seconds later, marshals took the correct decision to bring the race to a halt and Lorenzo's healthy lead in the championship was maintained.
I did think it may be a chaotic weekend and that is certainly how it turned out.
It is ridiculous over here in Malaysia - when it rains, it rains. It is like someone has turned a hosepipe on over your head. It is torrential - all the roads get flooded and then before you know it the sun comes out and it is dry again
It must have been horrendous for Lorenzo, who has been going into each race trying to nurse that lead and not take any chances.
But those wet and wild conditions are a recipe for things going wrong. It's so easy to make a mistake in wet weather and you only have to fall down and everything can change in the championship.
But there is still an ember burning for Pedrosa, a glimmer of hope.
His team-mate Casey Stoner said after the race that he fancied his own chances of winning if it hadn't been stopped.
If the heavy rain had stayed away for another 15 minutes we would have been in for a real grandstand finish.
Stoner put himself on the podium and I seriously wouldn't bet against him winning in Phillip Island next Sunday. Lorenzo won't want to push the boundaries too far and I think Stoner will certainly finish in front of him. It could be a cracking race between Stoner and Pedrosa because both will want to win desperately.
Dani wants to eat away at that championship lead again, little by little, and Stoner is determined to win at his home circuit in Australia for the sixth year in a row, and the final time before he retires.
It was disappointing for Cal Crutchlow to crash out and that means he has failed to finish four races out of the last six for various reasons, but he wasn't the only one. There were plenty of crashes.
MotoGP: Sandro Cortese wins Moto3 championship
The school report on Cal would say "could do better". He is riding really well, he is consistently on the pace but not finishing doesn't look good in the championship positions. He should be easily ahead of Valentino Rossi in the table but he has had a bad run at the wrong time.
In the earlier races, Sandro Cortese wrapped up the
championship with a win in a fantastic race as Malaysian rider Zulfahmi Khairuddin was unlucky not to hang on to win in front of a partisan crowd.
The Malaysian wildcard Hafizh Syahrin also had a great ride in the
race and it goes to show what some local success can do for crowds. There was amazing support, it was a bigger crowd than they get for Formula 1 and the main grandstands were sold out.
There is no rest for anyone as we head to Australia now in time for next weekend's penultimate race. Lorenzo leads by 23 points and can wrap up the title. Or will there be another twist?
Steve Parrish was talking to BBC Sport's Tom Rostance
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