RadioShack's team colours are red and grey.
However, seven-time champion Armstrong and his teammates showed up for the 20th and final stage wearing black outfits emblazoned with the number 28.
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That is a reference to the 28 million people Armstrong's Livestrong foundation estimates are living with cancer.
The American famously battled cancer in 1998 to return to racing and win the Tour seven times consecutively.
In recent years his Livestrong foundation has been involved in raising awareness, and funds, in a bid to beat the disease.
But his latest bid was kept in check by International Cycling Union (UCI) officials on Sunday.
After turning up wearing black for the 20th and final stage from Longjumeau to the Champs Elysees in Paris, the rest of the peloton had to wait while they were forced to change back to red and grey.
Race jury president Franceso Cenere told French TV: "It is forbidden to change jersey in a stage race without an authorisation from the UCI.
"They had to change jersey otherwise they would have been excluded from the race."
Armstrong decided to try again after the stage, when he and his team turned up at the podium to receive their prize for dominating the teams' classification wearing black.
"In the end, I think the fact we had to change the jerseys (before the stage) gave us some publicity," Armstrong told France Televisions.
On what was his final Tour campaign, Armstrong finished the race nearly 40 minutes behind Spain's three-time winner Alberto Contador, his former teammate at Astana in 2009.
The 38-year-old American is at the centre of serious doping allegations levelled recently by former teammate Floyd Landis.
Landis's accusations have led to the launching of a federal investigation into alleged doping practices of Armstrong and other riders at his former team, US Postal.
