AFL notified AFL Victoria that Essendon's VFL side would not be affected by the charges arising from the penalties announced on Tuesday.
Bombers chairman Paul Little indicated there would be no implications for the club's VFL side in his press conference.
The League also advised AFL Victoria the Essendon VFL side would be permitted to play in this season's VFL finals.
A statement on the VFL website confirmed Essendon was eligible to compete in the league's finals series.
Essendon's VFL side is scheduled to play against Werribee at North Port Oval on Sunday.
The club was aligned with VFL team the Bendigo Gold during the period of investigation in 2011-2012.
It decided to break that alliance and compete under the banner of the Essendon VFL team in 2013.
