The Spanish centre-back is recovering from a foot injury that he picked up against Spartak Moscow in the Champions League last month, but returned to training on Saturday afternoon.
"Pique has been out of action for quite a few days," said Vilanova.
"If he had at least trained in this time we would have more information and I am not in favour of [painkilling] injections because this could give us problems further down the line.
"There is no doubt about Pique's willingness to play because he has dedicated all the hours possible to recover but we cannot fight against nature."
Barcelona have won all of their six games in La Liga so far, while Madrid are eight points behind them in seventh.