Rasmussen extended his overall lead in cycling's most prestigious event before becoming the third cyclist to be dumped from this year's race because of a doping allegation.
Italy's Christian Moreni also was kicked out Wednesday, and Kazakhstan's Alexandre Vinokourov -- who tested positive after winning last weekend's time trial -- was kicked out earlier this week.
Vinokourov's team, Astana, later withdrew.
"I'm sorry the situation is coming out now, when I'm wearing the yellow jersey, and it's harming the sport that I dearly love," Rasmussen told the BBC.
The 33-year-old Dane missed out-of-competition drugs tests in May and June, and earlier denied he knew anything about doping questions. He has been dismissed by his Rabobank team.
"This is the saddest day in this sport," said team manager, Theo De Rooy.