The Repsol Honda rider crashed at Turn 1 around the halfway mark of the hour-long session, ending his day.
It marked the 2020 MotoGP world champion’s 12th crash so far this season, more than he had in the whole of 2022 while riding for Suzuki.
Honda said Mir had suffered damage around the fifth finger of the right hand, and would not continue with the weekend due to the “demanding nature of the Mugello Circuit.”
The team said: “Joan Mir had a difficult first day at the Italian GP, a crash mid-way through second practice ending his day early.
“Suffering significant discomfort, the #36 went to have his hand examined and revealed damage around the fifth finger of the right hand.
“Due to the high-speed and demanding nature of the Mugello Circuit, Joan Mir and the Repsol Honda Team have decided to withdraw from the remainder of the event due to the injury sustained to his right hand.”
Marc Marquez will now be the team’s sole factory rider for this weekend’s races, having returned from injury at the last round in France, where he was in podium contention before crashing.
Marquez finished eighth in the combined timings on Friday, guaranteeing him a place in Q2.
Alex Rins was the highest-placed Honda rider for LCR, finishing the day third, with team-mate Takaaki Nakagami in 21st.
Mir has scored just five points since joining Honda for 2023, all of which came at the season-opening Portuguese GP.
He was ruled out of the Argentina race the following weekend after crashing in the sprint, having been taken to hospital with cranial and cervical trauma.
Mir then crashed out of four consecutive rounds – the United States GP, both races in Jerez and in Le Mans.
Following his double crash at the French GP, Mir admitted he is “scared” of suffering the same fate as Jorge Lorenzo and Pol Espargaro at Honda given the difficulties he currently faces.
Mir is the fifth different rider in six years to partner Marquez at Honda, following Dani Pedrosa in 2018, Lorenzo in 2019, Alex Marquez in 2020 and Espargaro in 2021-22.
Pedrosa’s final year was his first winless one in MotoGP, while Lorenzo’s MotoGP career was effectively ended by the woes he suffered at Honda.
