The 2020 world champion crashed during the second practice session of the Italian GP weekend and fractured the little finger on his right hand.
He withdrew from the remainder of the Italian GP with the hopes of being fit enough to race at the Sachsenring this weekend.
However, Honda has now confirmed the Spaniard will take no part in the German GP, compounding what has already been a miserable season for him.
He will not be replaced.
Mir's move to the factory Honda squad after Suzuki quit MotoGP at the end of 2022 has been plagued by misfortune.
So far, he has scored just five points, having crashed out of the Portugal and Argentina sprints, the Americas GP, both contests in Spain and the grand prix in France.
His crash tally for the season has been 12, matching his own record from his rookie year in 2019.
Mir admitted after the French GP that he was "scared" about repeating the failures at Honda experienced by the likes of Jorge Lorenzo and Pol Espargaro, who both endured torrid years on the RC213V at the factory squad.
The 2020 world champion won't be the only Honda rider absent from the German GP, after LCR's Alex Rins broke his right leg in a crash in the sprint race at Mugello.
Rins, who is Honda's only winner in 2023 having taken victory in the Americas GP, had to have an external fixator attached to his leg.
He has now flown home to Spain and will undergo further surgery later this week on his leg, but will be out of action until August's British GP at the earliest.
LCR will not replace Rins this weekend in German, meaning Honda will be represented by Marc Marquez at the factory squad and Takaaki Nakagami at LCR.
After crashing out of the Italian GP, ensuring a 100% non-finish record in Sunday races in 2023, Marquez admitted the constant falls he is having because of the Honda are "difficult on the mental side".
