The factory Yamaha rider sustained injuries to his ring and middle fingers.
A decision is yet to be taken over whether Lorenzo will contest the final race of the season in Valencia, Spain, on 6 November.
Lorenzo added: "I am very proud of my team for all the hard work they have put in to take second in the championship.
"Now we have to think about next year and work as hard as possible to win again."
Yahama confirmed in a statement that Lorenzo was out of the Malaysian Grand Prix. They added: "The surgeon was able to save the nerves and tendons of the injured fourth finger and, as a result, no functionality will be lost in either the finger or the hand.
"A decision on the Valencia Grand Prix will be made dependent on Jorge's condition after his return to Barcelona."
Lorenzo's Yamaha team-mate Ben Spies also missed the Australia race after a crash in qualifying.
Yamaha said: "After attempting to ride some laps in warm up, the rider reached an agreement with team members that attempting the race with reduced concentration would be considered too dangerous for himself and other competitors."
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