Once repaired, he had to fight his way back through the field as he attempted to catch up with Contador, but was unable to make up the lost ground, finishing 39 seconds behind the Spaniard.
Schleck said that cycling etiquette dictates that Contador and other riders should have waited for him, as happened when he crashed earlier in the race.
"Today, you know, everybody is in panic, they see already the Eiffel Tower. I would not have taken advantage of the situation," he said.
"It's not up to me ... but for sure these guys don't get the fair play prize today."
Contador said that the issue would not decide the outcome of the Tour.
"I planned to attack anyway, and when I knew what had happened to him I was already ahead and racing," he said.
"Of course I know it's a delicate situation and could lead to debate, but I don't believe that to lose or win 30 seconds at this point will make you win or lose the Tour de France."
In the end, Contador took an eight second overall lead from Monday's stage. But the honours went to French champion Thomas Voeckler, who claimed his second stage win on day two in the Pyrenees.
The riders are now preparing for Tuesday's 16th stage, which is one of the toughest mountain sections of the course.