"Michael Rasmussen has been sent home for violating (the team's) internal rules," Rabobank team spokesman Jacob Bergsma told The Associated Press by phone.
The expulsion, which Bergsma said was ordered by the Dutch team sponsor, was linked to "incorrect" information that Rasmussen gave to the team's sports director over his whereabouts last month. Rasmussen missed random drug tests May 8 and June 28.
The 33-year-old rider, who won Wednesday's stage, had looked set to win the race, which ends Sunday in Paris. But Tour officials had questioned why he was allowed to take the start on July 7 in London, England.
"We cannot say that Rasmussen cheated, but his flippancy and his lies on his whereabouts had become unbearable," Tour director Christian Prudhomme told the AP.
The leader of cycling's governing body applauded the decision.
"My immediate reaction is, why didn't they do this at the end of June, when they had the same information," Pat McQuaid said. "The team decided to pull him out; that's their prerogative. I can only applaud that. It's a zero-tolerance policy, and it's a lesson for the future."
With Rasmussen out, Spanish rider Alberto Contador of the Discovery Channel team moved into the race lead.
"It's in no way a celebration on our end. It's the third piece of bad news," said Discovery Channel spokesman P.J. Rabice. "It reflects badly on our sport."
After the Tour's upbeat start in London, when millions of spectators lined the streets, bad news - nearly all of it related to doping - quickly claimed the spotlight.
On Tuesday, star cyclist Alexandre Vinokourov was sent home after testing positive for a banned blood transfusion, and his team pulled out of the race. Wednesday, it happened again when the Cofidis squad confirmed its rider Cristian Moreni of Italy had failed a doping test, prompted the withdrawal of the entire squad.
It wasn't immediately clear whether the 104-year-old Tour ever had lost its leader in such fashion so close to the finish.
"In the very old history of the Tour de France, I don't know, but the recent past - never," said Tour spokesman Philippe Sudres.