Dundee also went into administration in 2003 when they were in the Scottish Premier League.
The SFL also plan an early-warning system with HMRC to alert them to any more clubs facing financial difficulties.
"We are fully aware of the impact this situation has had on all concerned, especially players, staff and fans of the club," added SFL chief executive David Longmuir.
"The SFL has a duty to protect the integrity and the ongoing smooth running of the league.
"Following a thorough process, as endorsed by the administrator, the board has decided that Dundee Football Club Limited is guilty of conduct contrary to the league rules, the interests of the league and its member clubs."
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