Rins, who required surgery after fracturing his tibia and fibula at Mugello, completed 16 laps in the morning but just 6 in the longer, one-hour, afternoon practice.
LCR Honda then confirmed that the Spaniard ‘has been declared unfit due to the pain he’s felt today on the right leg while testing on track.’
Rins, joining Monster Yamaha next season, had admitted after passing a medical check on Thursday:
"If it’s painful then it won’t make sense to continue riding.
“I’m still not 100% recovered but it’s going step by step. The next step is to try the MotoGP bike.
“It’s been one month without trying any bike. Let’s see what the reception is like on the bike."
Last in both Friday sessions, the COTA race winner was a respectable +2.395s from Jorge Martin in the morning before dropping +3.747s from Brad Binder's new lap record after his handful of afternoon laps.
HRC test rider Stefan Bradl, who was again due to replace Rins before the Spaniard's last-minute trip to Motegi, will now take over the RCV on Saturday.
Meanwhile, Rins will try again at the upcoming Indonesian round, from October 13-15.