Wilson was sent off for denying a goalscoring opportunity when Rangers won the 2010 final against St Mirren and was automatically suspended for his next game in the competition.
Wilson signed for Liverpool three months later before Rangers began the defence of their trophy and left without serving the ban.
He returned to Scotland this month on a loan deal and made his second Hearts appearance as John McGlynn's side beat Inverness on penalties at Easter Road to reach the Scottish Communities League Cup final.
An Inverness statement read: "We have spoken to the SFA disciplinary committee who have confirmed that Danny was eligible to play on Saturday.
"This was checked out by Hearts and the SPL prior to Saturday's game.
"There was no notice of suspension accompanying his registration paperwork when he returned from Liverpool FC."
Wilson made his Liverpool debut in the Anfield team's opening League Cup game of the 2010-11 season, a penalty shootout defeat in September against Northampton, for whom Inverness striker Billy McKay scored in a 2-2 draw.
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