The Ghanian was starting in midfield alongside Mohamed Elneny after his Man of the Match performance in a 1-0 win against Manchester United last Sunday.
The 27-year-old has impressed since joining the Gunners in a £45million deal from Atletico Madrid but he lasted just 45 minutes against Dean Smith’s side, who took a 1-0 lead into the break after an own goal from Bukayo Saka.
The decision came as a surprise, as many felt it would be Elneny that was taken off for Dani Ceballos as Arsenal searched to overturn the deficit.
However, Premier League Productions quickly confirmed after the interval that Partey had been taken off as a precaution.
The Ghanian was seen holding his left thigh shortly before the break and Mikel Arteta clearly felt it was not worth risking the midfielder after the restart.
‘We understand he has an ice pack on his left thigh so he has picked up an injury,’ said the Premier League Productions commentary team.
‘It’s not what Arsenal fans want to hear.’
The Black Stars face Sudan twice in four days, before taking on South Africa.
The day went from bad to worse for Arsenal as Ollie Watkins scored twice in the second half to put Villa 3-0 up with ten minutes to go at the Emirates.