Ji, 22, made four league appearances in 2013-14 before leaving for Augsburg in January, the striker agreeing terms for a summer move to Borussia Dortmund a day later.
The Premier League strugglers – who are second from bottom in the table – claimed an administrative error led to the blunder.
And Sunderland officials have been left red-faced after being handed a fine for the incident, which they confirmed they were made aware of in December, paying the subsequent penalty earlier this year.
The Wearsiders will be relieved, however, to have escaped further punishment in the form of a points deduction, which would have severely dented their survival hopes.
"There was an administrative issue regarding the registration of the player," said a club statement released to ITV.
"The club was fined by the Premier League and the matter was dealt with at the time."
The Black Cats also fielded Ji against MK Dons on their march to the League Cup final, prompting a second fine from the Football League.