Laverty was last of the 18 runners in this morning's first practice, and was 3.3 seconds off the pace as he attempted his first laps aboard his Ducati V4 R Panigale in almost two months.
He carried on into the second 50-minute session in the afternoon, and improved his laptime by seven tenths to a 1m30.409s to reduce his deficit to pacesetter Tom Sykes on the BMW to 2.6s.
However, after further medical evaluation after Friday's running, Laverty has been declared unfit to continue.
It is unclear yet if the Go Eleven team will field a replacement for the remainder of the weekend.
British Superbike frontrunner Tommy Bridewell – who riders a V4 R in Moto Rapido colours - deputised for Laverty at Imola and Jerez, but opted out of doing so again at Misano having just taken the lead in the BSB standings.
Ducati test rider Lorenzo Zanetti was called up to fill in at Misano, and managed two ninth-place finishes in both feature races, as well as a 10th-place finish in the Superpole race.
Laverty revealed on social media this week he had intended to stage his comeback at next weekend's US round at Laguna Seca, but it is not known if this latest setback will force him to miss the final event prior to the summer break.
Yamaha's Michael van der Mark, who had fractured his wrist in a crash at Misano, will continue on this weekend and was 11th overall on Friday after failing to improve on his FP1 lap in the afternoon.