It claimed that Santos vice-president Odlio Rodrigues said Guardiola had encouraged Neymar to sign for Bayern instead of Barcelona, telling the player's father that Vilanova would be unable to manage having both the Brazilian and Lionel Messi in the same team.
Guardiola denied the story, saying: "I don't know the vice-president of Santos but probably his intermediaries have got this very wrong, because the information they have given him is false.
"I would never make any comments like those he said I made."
He admitted speaking to the player's father in New York when he became the Bayern coach "to see what his situation was".
He said: "In that meeting and in the two conversations we had before that I must have told him 20 times how well he would do at Barcelona, and in none of those three meetings did the name Tito Vilanova come up.
"It's not necessary for me to say if he [Vilanova] is a capable coach or not, he was my assistant for five years and what he did last year speaks for itself, because he led the club to their greatest season in their history.
"What's more, the best players can always play together and those two [Neymar and Messi] are capable of playing together for many years."