He crossed the line in Angers in 77th place but in the same time as stage winner Mark Cavendish (Dimension Data) and all his main GC rivals.
"Today was more or less okay but I've not been able to ride well because I can't go too much on the pedals because of the pain in my legs," Contador told Cyclingnews in between swigs from a bidon as he stood on the finish line.
"Now it's my left leg that gives me problems after my crash yesterday."
Contador crashed on the opening stage, hitting his right side with tremendous force and sustaining superficial wounds. Nothing was broken but the impact of the fall has put him in trouble. On stage 2, he fell again, this time in the wet with several riders landing on top of him. He conceded 48 seconds that day after he was unable to hold the favourites on the climb to the line.
His priority, he stressed at the finish in Angers, was to recover as quickly as possible. Stage 4 looks set for another sprint stage but stage 5 sees the race entertain its second uphill finish. Contador can ill afford another bad day and he will be praying for another slow day as he and the rest of the peloton experienced on the road to Angers.
"I know that I'm not feeling better than yesterday but I'm still here," he said.
"The priority now is to get to the hotel as soon as possible so that I can start to recover again. This Tour, and in this moment, it's very difficult for me but it's only stage 3 of 21 and I still have my morale even after my crashes."