The 24-year-old ex-North Melbourne player, who was sacked from the team in February over repeated conduct breaches, faced Broadmeadows Magistrates Court on Thursday.
Thomas, who also uses the surname Trindall, pleaded guilty to breaching a court order involving repeated calls to a victim in April, the court was told.
But police withdrew the harassment charge.
Six of the calls were answered by the victim, who reported hearing heavy breathing on the other end of the line, the court was told.
Police seized Thomas' phone in May after a search at his Ormond address, which revealed it to be the phone used in the alleged calls.
Magistrate James Henderson handed Thomas a 12-month good behaviour bond on the condition he continued therapy with both a psychologist and psychiatrist.
Thomas' guilty plea and work to rehabilitate himself through therapy and connecting with culture were taken into account in the decision.
The court was told Thomas' father, who was abusive and had substance misuse issues, had prevented a 10 or 11-year-old Thomas from seeing his mother for years after the parents split.
"Both medical professionals identified that Mr Trindall has suffered developmental trauma as a result of experiences he had as a child, that those experiences have negatively impacted his behaviour, his understanding of appropriate relationships," Thomas' lawyer Sally Vary said.
"He lacked role-modelling. He lacked a familial bond. He lacked care, essentially throughout that period of time, in those formative years."
Thomas was sacked after being suspended for 18 games by the AFL, which confirmed in May he could not play or train at any level of the game without the league's approval.
The AFL has been contacted for comment.
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