"I send you my warmest congratulations on becoming the first British cyclist ever to win the Tour de France," read the message on the queen's official website posted on Monday.
"Your historic achievement of claiming overall victory in this prestigious event is a great testament to the efforts of you and your team-mates."
Wiggins' success, as well as teammate Chris Froome's second place finish on the tour, has boosted hopes of more cycling gold for Britain in the London Olympic Games.
In recognition of Britain's current domination in the sport, triple gold medal track cyclist Chris Hoy will carry the British flag at the opening ceremony on Friday.
Just 24 hours after completing the gruelling 3,479-km race, Wiggins was back in the saddle on home soil preparing for the men's time-trial and road race events.
He spent a few hours with his family before hitting the roads around his home in Chorley, Lancashire, sporting the yellow helmet and sunglasses he wore during the Tour.
The road race in particular will take Wiggins over more historic territory and as the event whizzes by Buckingham Palace, he may even get a wave from the queen herself.