The Movistar sprinter took third at the finish line behind winner Mark Cavendish (HTC-Highroad) and Philippe Gilbert (Omega Pharma-Lotto) and was actually presented with the green jersey as points classification leader for the third day in a row. Any celebrations were short-lived with Tour commissaires announcing an infringement by the Spaniard during the day's intermediate sprint at 70 kilometres.
"After reviewing the intermediate sprint it has been decided by the race jury to relegate Jose Joaquin Rojas and Tom Boonen from the intermediate sprint," said the race's competition director, Jean-Francois Pescheux.
"Both riders blocked Cavendish when he was trying to race up the inside. As a result both riders lose the points.
"The green jersey now goes to Philippe Gilbert."
The overhead shot of the sprint to the line showed Cavendish following the wheel of the Movistar man, with Boonen to the Spaniard's left. As Rojas veered to the left, Boonen too was forced across the road, and Cavendish's path was blocked.
The initial points breakdown at the intermediate sprint awarded sixth-placed Boonen with 10 points, Rojas (ninth) therefore earning 7 points, while Cavendish, who took out his frustration on his handlebars, was 13th with 3 points. Upon review, Cavendish added five points to his tally.
The decision and reallocation was enough to catapault Gilbert into the points lead (120) with Rojas eight points in arrears.
Newly-crowned Spanish road champion hit out at the action via his Twitter feed -
"And this is the best race in the world? God I come and see it! Disqualified because they feel like, well, more like Gilbert ..."
However, the 26-year-old's scathing attack didn't end there, claiming Lampre's Alessandro Petacchi used underhand tactics against him in the run in to the stage finish.
"I was confident for the sprint, I had good legs and was looking for Cavendish's when Petacchi punched me with just over one kilometre to go," Rojas said via a statement.
"I could hardly breathe and that's why I failed to beat Cavendish. Anyway, we're talking about one of the best sprinters in history of the sport and to even rub shoulders with him is satisfying. I'll take that result. I keep proving to people who don't think I can win the green jersey that it is possible."