The Italian was absent from the squad as Liverpool's UEFA Champions League hopes suffered a huge blow in a 4-1 loss at the Emirates Stadium.
Rodgers explained: "He trained yesterday afternoon with the team and he took a knock, a slight knock to his knee, and he deemed it not able to travel with the team."
Balotelli drew criticism from his manager in February, when the forward's late penalty secured a 1-0 win over Besiktas.
In that instance he took the ball from Jordan Henderson, but it was the Italy international's application that troubled Rodgers, who said "once we get the penalty, Mario stops working".
The 24-year-old has scored only one league goal this season.
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