The 2020 world champion was forced into a recovery ride in Saturday's 12-lap sprint after struggling to 18th and last on the depleted grid in qualifying.
On the opening lap, Mir crashed heavily going through Turn 7 and had to be taken to the medical centre for a check-up.
Initial scans revealed no serious injuries, but he was taken to hospital in Santiago del Estero for further checks on his right ankle.
Though no major damage to his ankle was detected, Mir - together with Honda – have decided to withdraw from the remainder of the Argentina weekend in order for him to be fit for the Americas GP on 14-16 April.
It means no factory Honda team rider will be present on a MotoGP grid for the second time in two seasons, having gone unrepresented at the 2021 Valencia GP.
A brief statement from Honda read: "The Repsol Honda Team and Joan Mir have together decided to sit out the remainder of the Argentina Grand Prix weekend to allow the #36 to rest and recover.
"He will return home to Europe to continue his recovery to be fully prepared for the Grand Prix of the Americas, 14-16 April.
"No major injuries were detected in the tests done at the circuit and in Santiago del Estero hospital, but the Repsol Honda Team rider reported significant discomfort and pain after the heavy impact associated with the fall."
With just 17 riders starting Sunday's grand prix at Rio Hondo, it will mark the smallest grid for a race since the 2011 season.
That year, there were two events in which only 15 riders started, while in Australia that number shrank to 14.
The factory Honda squad was already down a rider coming into the Argentina GP, after Marc Marquez was forced to the sidelines by a hand fracture he suffered in a controversial crash with Miguel Oliveira in the Portuguese GP.
With Mir's absence, five full-time riders will now miss this year's Argentina GP, with injuries also forcing Pol Espargaro, Oliveira and Enea Bastianini out pre-weekend.
Gresini's Alex Marquez will start on pole for this afternoon's Argentina GP, while sprint winner Brad Binder will once again have to fight through from 15th.
