The Irn-Bru First Division team failed in an appeal to the Scottish Football Association after the Scottish Football League upheld their original decision last year.
Dundee's position at the bottom of the table is now confirmed, although they could yet challenge the decision in a court of law.
A Scottish FA statement read: "At a meeting of the Scottish FA's appeals sub-committee, the following decisions were taken in relation to Dundee Football Club's appeal of sanctions imposed by the Scottish Football League:
"1. Dundee's appeal against a deduction of 25 championship points for season 2010-2011 was rejected
"2. Dundee's player registration embargo will remain in place until the club comes out of administration."
Dundee chief executive Harry MacLean said the Dark Blues would have to turn their focus to surviving on the pitch.
"Our initial reaction is severe disappointment, but we don't want to go into it too deeply at this point," he said.
"We've been to the Scottish Football League, we've been to the SFA and as things stand we're just probably going to have to abide by the decision, pick ourselves up and get on with it and try and get up the season a little bit before the season finishes."
Dundee have dropped from second place on 32 points to 10th on seven. They are five points behind Stirling, who have won three of their 15 games all season, at the foot of the First Division table.
Source: PA
Source: PA