The 33-year-old Spaniard suffered stage one and two crashes, resulting in damage to a hamstring, shoulder and thigh, and quit the race 100km from the end of the ninth stage because of fever.
Rio de Janiero's Olympic road race takes place on 6 August on a hilly course that is well suited to Contador but as this comes too soon, he will attempt to make a comeback at the Vuelta a Espana, which starts on 20 August.
"Reaching the Olympics is a challenge in itself, added to that is getting there in optimal condition.
"It looks like it will not be possible.
"My goal now is to recover for the Vuelta."