Lorenzo, the 2010 world champion, is recovering in Barcelona after undergoing plastic surgery on his left ring finger following his crash in the warm-up for last weekend's Australian Grand Prix.
The Spaniard will not be fit in time to race at Sepang, so Yamaha have taken the decision to hand Nakasuga a MotoGP debut in his absence.
Nakasuga, 30, has also been competing in the All Japan Road Racing Championship, JSB1000 class, and is third in the standings.
A Yamaha statement confirming the decision read: "Yamaha YZR-M1 test rider Katsuyuki Nakasuga has been drafted in to replace injured Yamaha Factory Racing star Jorge Lorenzo for this weekend's Grand Prix of Malaysia."
A decision on Lorenzo's fitness ahead of the season finale in Valencia will be taken within the next two weeks.