He had won Le Tour, except he -- and everybody else -- just didn't know it yet.
Instead, the yellow jersey, champagne and flowers that day went to American Floyd Landis, who wrestled the race lead back from Pereiro on the penultimate stage after an engrossing back and forth.
However, once the Tour was over, one of Landis' urine sample "A" tests from the race came back positive for an unusually high level of testosterone.
Pereiro initially said he had "too much respect" for his opponent to consider him a cheat after the American's first positive test.
When Landis' "B" sample also came back positive, he was eventually stripped of his 2006 Tour de France win and the title was awarded to the then runner-up, Pereiro.
Landis, the first Tour de France winner stripped of the title
, initially maintained his innocence but later admitted to doping and accused others, including Lance Armstrong, of doing the same.
The Spaniard now holds no resentment towards the past, but admits the victory feels somewhat bittersweet after the way events unfolded.
"A lot of time has passed," he tells CNN, now sounding philosophical. "The answer is always the same: sadness for not having been able to enjoy it at the time.
"But at the end of the day, look, things come as they come and one needs to remember the moments you had on the bike. Everything that happened with Floyd's positive test came after.