Pantani, who died in 2004, won the controversial race, with Ullrich taking second place.
The commission, though, found no hard evidence that American Bobby Julich, who was third, also used EPO, as Le Monde newspaper had reported Tuesday.
The findings were based on comparisons made of retrospective testing results from 2004 and a list of samples from the 1998 Tour de France and the 1999 race won by disgraced US rider Lance Armstrong.
Armstrong was stripped of his seven Tour wins and banned from cycling for life last year for doping in a scandal that plunged cycling into crisis about the extent of substance abuse among the peloton.
The commission compared the results from the anonymous samples from 2004 to named samples taken from the two Tours under scrutiny.
Aside from Pantani and Ullrich, a trio of French riders were also found to have used EPO in the 1998 Tour – Laurent Jalabert, Jacky Durand and Laurent Desbiens, the commission's report revealed.
In May, Jalabert was identified as an alleged doper and he immediately stepped down as a television and radio pundit for this year's Tour that was won last Sunday by British rider Chris Froome.
Since then, there has been debate in France about the utility of naming names, with the family of Pantani saying they were against identifying riders.
The professional cyclists' union the CPA last Friday said that it, too, was opposed to publication.
"Publication of a list amounts… to an accusation of doping without any means of defence," the union said, arguing that no counter-analysis was possible as the original samples no longer existed.
Pantani, who won both the Tour of Italy and Tour de France in 1998, never tested positive throughout his career, although he was expelled from the 1999 Giro due to irregular blood levels.
Ullrich for his part held his hands up to doping in June.
The commission questioned 84 witnesses under oath, from sportsmen and women to organizers and anti-doping experts, to "lift the lid" on and "break the code of silence" over the subject.
Cycling, with its doping-scarred past, has not been the only focus, however, with attention also paid in particular to rugby.
The French anti-doping agency assessed that the sport was the most affected by doping in relation to its testing, while football and tennis were also examined.
France football coach Didier Deschamps was questioned behind closed doors while tennis came under the scanner for its relative lack of testing at an international level.
The senators are aiming to frame legislation on sport and put it before parliament for debate next year.