The samples contained synthetic testosterone, indicating that it came from an outside source.
"I have received a text message from Chatenay-Malabry lab that indicates the 'B' sample of Floyd Landis' urine confirms testosterone was taken in an exogenous way," Pierre Bordry, who heads the French anti-doping council, told The Associated Press shortly after the "B" sample results were released.
Lab head Jacques De Ceaurriz said the isotope testing procedure was "foolproof."
"No error is possible in isotopic readings," he told the AP.
Landis, of Murrieta, Calif., had claimed the testosterone was "natural and produced by my own organism," and once again maintained his innocence.
"I have never taken any banned substance, including testosterone," he said in a statement. "I was the strongest man at the Tour de France, and that is why I am the champion.
"I will fight these charges with the same determination and intensity that I bring to my training and racing. It is now my goal to clear my name and restore what I worked so hard to achieve."
But Dr. Gary Wadler, an expert on athlete drug use, told CBS News correspondent Randall Pinkston that it's unlikely Landis will be able to prove his innocence. "Something happened the day he tested positive. Somehow testosterone levels shot up and they don't just shoot up from changes in your own body."
The Swiss-based team Phonak immediately severed ties with Landis, and the UCI said it would ask USA Cycling to open disciplinary proceedings against him.
"Landis will be dismissed without notice for violating the team's internal Code of Ethics," Phonak said in a statement. "Landis will continue to have legal options to contest the findings. However, this will be his personal affair, and the Phonak team will no longer be involved in that."
Tour de France director Christian Prudhomme said Landis no longer was considered champion, but the decision to strip him of his title rests with the International Cycling Union.
"It goes without saying that for us Floyd Landis is no longer the winner of the 2006 Tour de France," Prudhomme told the AP in a telephone interview. "Our determination is even stronger now to fight against doping and to defend this magnificent sport."
Prudhomme said runner-up Oscar Pereiro of Spain would be the likely new winner.
"We can't imagine a different outcome," Prudhomme said.
If stripped of the title, Landis would become the first winner in the 103-year history of cycling's premier race to lose his Tour crown over doping allegations.
Documentation from the positive tests will be forwarded to the U.S. Anti-Doping Agency, which gives the evidence to a review panel. The panel will make a recommendation to USADA, which would decide if a penalty — likely a two-year ban — is appropriate. That decision is forwarded to USA Cycling, the UCI and the World Anti-Doping Agency. Landis can accept the decision or begin an appeals process, which can take up to six months.
"Until he is found guilty or admits guilt, he will keep the yellow jersey," he said. "This is normal. You are not sanctioned before you are found guilty."
The results of the second test come nearly two weeks after he stood atop the winner's podium on the Champs-Elysees in the champion's yellow jersey.
Testosterone, a male sex hormone, helps build muscle and improve stamina. The urine tests were done July 20 after Landis' Stage 17 victory during a grueling Alpine leg, when he regained nearly eight minutes against then-leader Pereiro — and went on to win the three-week race.
The tests turned up a testosterone/epitestosterone ratio of 11:1 — far in excess of the 4:1 limit.
On The Saturday Early Show, Steve Madden, editor-in-chief of Bicycling Magazine, told co-anchor Russ Mitchell that the test results were tough to handle.
"I still want to believe him," Madden said. "I feel like I still need to believe him."
"It's incredibly disappointing," three-time Tour winner Greg LeMond said by phone from the starting line at the Pan Mass Challenge in Sturbridge, Mass. "I don't think he has much chance at all to try to prove his innocence."
"It doesn't end here," said Landis' Spanish lawyer, Jose Maria Buxeda. "What matters is the concept. A prohibited substance has been found in the samples, but no immediate sanction comes into effect yet. The rider will defend himself."
Landis, a 30-year-old former mountain biker, says he was tested eight other times during the three-week tour and those results came back negative.
Landis has hired high-profile American lawyer Howard Jacobs, who has represented several athletes in doping cases.
Jacobs plans to go after the UCI for allegedly leaking information regarding the sample testing.
Earlier this week, a New York Times report cited a source from the UCI saying that a second analysis of Landis' "A" sample by carbon isotope ratio testing had detected synthetic testosterone — meaning it was ingested.
"The offense is complete," World Anti-Doping Agency chairman Dick Pound said. "All that remains to be seen is what the sanction is.
"A doping offense occurs when a presence of a prohibited substance is detected in the urine or blood analysis. That's been done," he said.
Since the Phonak team was informed of the positive test on July 27, Landis and his defense team have offered various explanations for the high testosterone reading — including cortisone shots taken for pain in Landis' degenerating hip; drinking beer and whiskey the night before; thyroid medication; and his natural metabolism.
Another theory — dehydration — was rebuffed by anti-doping experts.
"When I heard it was synthetic hormone, it is almost impossible to be caused by natural events. It's kind of a downer," said LeMond, the first American to win the Tour. "I feel for Floyd's family. I hope Floyd will come clean on it and help the sport. We need to figure out how to clean the sport up, and we need the help of Floyd."
In Murrieta, Calif., where Landis lives, an AP reporter was asked by police to leave the gated community when she attempted to approach his house. Several cars were parked in front, and the blinds were drawn.
A man who said he was a friend of the family, but didn't want his name used, answered the phone at the Landis' house and confirmed the cyclist was there.
"We're drinking some coffee, and that's about it," he said.
Despite the latest test results a sign at a nearby freeway exit said, "Welcome Home Floyd Landis, 2006 Tour de France Winner."
In Lancaster County, Pa., where Landis was raised in a conservative Mennonite home, neighbors vowed their support.
"All he has accomplished, he has attained through his hard work and discipline. We are very confident he will prove his innocence. It is very unfortunate that these tests were revealed before he had a chance to do so," said Tammy Martin, a longtime family friend.
Paul and Arlene Landis, who have supported their son since the doping scandal broke, were out of town on a previously scheduled vacation.
A note on their door said, "God Bless, Went Camping."