Scottish Football League chief executive David Longmuir announced their punishment on Monday following a meeting of the organisation's board.
Dundee have also been hit with a player registration embargo and the SFL will reconsider their situation if they are not out of administration by March 31.
The SFL also plan an early-warning system with Her Majesty's Revenue and Customs (HMRC) to alert them to any more clubs facing financial difficulties.
Dundee went into administration on October 14 after being unable to pay a tax bill which stood at ¦pound;420,000.
Longmuir said: "The SFL regrets the situation Dundee Football Club find themselves in for the second time in seven years.
"We are fully aware of the impact this situation has had on all concerned, especially players, staff and fans of the club. 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.
"The following sanctions will be imposed. Dundee Football Club will be deducted 25 league championship points with immediate effect, a player registration embargo be imposed until the club comes out of administration, and if the club is still in administration by March 31, the board will reconsider the matter and will deal with the club as it sees fit.
"It should be noted that Dundee Football Club has the right of appeal against these sanctions."
Source: PA
Source: PA