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The 29-year-old played a full part in Wednesday's 1-0 Africa Cup of Nations qualifying win over the same opponent, but was not called upon for Tuesday's 1-1 draw in Talatona.
Ghana head coach Chris Hughton later explained Partey, who missed two Arsenal games in February with a back injury, was not risked due to a minor problem.
"Thomas has some small issues," Hughton said. "We felt it was too big of a risk to start him."
Partey, who was accompanied on Ghana duty by Arsenal physio Simon Murphy, has played in 30 of the Gunners' 39 games this season.
Premier League leader Arsenal is back in action on Sunday with a home match against Leeds United, before travelling to Liverpool eight days later.