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.
"You can't look back anymore, I would have liked things to be different but, in the end, the only thing you can think is that life is like that, things happen as they do and thinking about it won't change it.
"I feel like a Tour de France winner exactly like any other winner."
'We lost all of that'
Pereiro describes any cyclist's efforts on a bike as "50% mental and 50% physical."
For the winner of the Tour de France, considered by many one of the toughest athletes on the planet, those efforts are rewarded with a celebratory final stage.
Champagne is often served by team leaders and, with the overall classification sewn up, the rider in the yellow jersey can enjoy the final day, crossing the line on the iconic Champs-Élysées.
Pereiro, despite being denied that special day, is more than content with how his career panned out.
"It gave me a lot of sadness because when I see the victories of riders who win Le Tour, that day is very special," he explains. "Not only for you, but for your team, your family. We lost all of that.
"But over time you realize it's not worth it to keep thinking about the past because you can't change it.
"So for me, what's important today is being recognized as the winner, the people that call me to work and the people that still follow me and say, 'what a great career you had.'"
Life after cycling
Given that riders in the Tour de France can burn upwards of 4,000 calories a day, one of the main problems facing retired cyclists is often an expanding waistline.
Pereiro, keen to temporarily get away from cycling once he retired in an attempt to "open his mind," decided to pursue the sport he first played as a kid: football.
After a conversation with the president of Coruxo, a fourth-tier Spanish club in Vigo, near to where Pereiro was born, the then 33-year-old was convinced to start training.
To say it went well on a personal level would be an understatement. Pereiro played two games, scoring two goals. Not a bad ratio for a retired cyclist.
"When I decided to retire I wanted to keep playing sports, I didn't want to get fat!" he recalls. "I wanted to take part in a sport that was different to cycling. It was another experience.
"The level wasn't good enough to play in the first division (La Liga), it was very bad. Very bad, very bad but I had fun there and it went really well."