Villa were found guilty by the Premier League of their ball-boys on several occasions handing the ball to Villa players, rather than follow the rules and let them collect it from cones around the pitch.
The rules were broken over the final five games of last season.
The EPL stated: "Clubs are required to adopt a multi-ball system at every league match and adherence to the relevant rules and guidance is of vital importance to maintain consistency and, crucially, to ensure that home clubs do not gain a competitive advantage through their misuse of the system.
"The club will pay a £125,000 fine and will be prohibited from operating the multi-ball system in its first three home league matches of the 2025/26 season."
