They were the most high-profile casualties yesterday as the organizers attempted to make a clean break with those riders and teams linked to recent drug scandals by inviting squads committed to building a new generation of stars, preferably French.
Pantani reacted bitterly to the announcement.
"The bosses of the Tour are killing cycling," he said. "My exclusion and that of Cipollini mean the race will die."
Yesterday, the final four teams for the race were due to be announced, taking the total to 20. Instead, the field was unexpectedly stretched to 21 teams and 188 riders to accommodate two French squads, BigMat-Auber 93 and La Franaise des Jeux, and a Basque team, Euskaltel, all of whom have strong youth policies.
There will be eight French teams, more than for at least a quarter of a century.
Pantani's Mercatone Uno, Cipollini's Saeco-Macchine da Caffe and the German squad Team Coast, which includes Alex Zlle and Fernando Escartin, second and third in 1999, were rejected.
"This is a break with the cycling of one era and opens the way for a new approach and a new state of mind," said the Tour organizer, Jean-Marie Leblanc.
This was as close as he came to saying that the action was all about cleaning up the Tour. Pantani has been found guilty of sporting fraud by using banned drugs and, although Cipollini has not been involved in any malpractice, Saeco's stage winner in last year's Tour, Salvatore Commesso, is currently banned and their candidate for a high Tour placing overall would have been Laurent Dufaux, one of the nine Festina riders thrown off the race in 1998.
There is a chance of a third British entrant alongside David Millar and Max Sciandri. The Devon sprinter Jeremy Hunt, who rides for BigMat, is recovering from injury but now has a chance of a place in his first Tour.
Want to ride 100 miles?Check out our Century Challenge section