Thomas, 24, is also not eligible for the 2025 mid-season draft while no decision has been made on whether he can return to the AFL next year.
The former Kangaroo had been ineligible to play football at any level after an AFL integrity unit investigation last February found he had engaged in multiple acts of misconduct, including threatening a woman in direct messages.
He was suspended for 18 matches and subsequently axed by North Melbourne.
In November, Thomas walked free from court on a good behaviour bond, avoiding a criminal conviction after police dropped a charge of using a telecommunications service to harass a woman.
The AFL confirmed on Thursday Thomas was now eligible to play for stand-alone clubs in the VFL, SANFL and WAFL after showing a "consistent change in his behaviour" and completing an education and behavioural change program.
In the VFL, he could therefore play with Coburg, Frankston, the Northern Bullants, Port Melbourne, Southport, Werribee or Williamstown as he attempts to restart his career.
Thomas is eligible to feature for any SANFL club bar Port Adelaide and Adelaide's teams, and for WAFL teams apart from West Coast or Peel Thunder, who are Fremantle's affiliate.
"The AFL has been kept up to date with Thomas' progress, which has included his completion of a comprehensive education and behavioural change program, and importantly a consistent change in his behaviour over a period of time," an AFL spokesperson said in a statement.
"To be clear, Thomas is not approved to play in the AFL competition in 2025 or for any club with an AFL affiliation in a state league competition, however as part of his rehabilitation he has been approved to play in football competitions below the AFL.
"He will also not be eligible for the 2025 AFL mid-season draft.
"No decision has been made in relation to Thomas' eligibility to play in the AFL in 2026 or thereafter and that matter is not presently under consideration."
St Kilda head of talent and acquisition Graeme Allan met with Thomas last August but the club decided against pursuing him following backlash over the meeting.
Essendon distanced themselves from Thomas in a letter to members in June, after coach Brad Scott had described the player as a "good person".
Thomas, the No.8 draft pick in 2018, played 69 games for North Melbourne from 2019 to 2023.
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