Jupp Heynckes will step down as the Bavarian boss at the end of the season and the former Blaugrana man will take over having been out of football since stepping down at the Camp Nou at the end of the 2011-12 campaign.
Vilanova revealed to reporters after Barcelona’s 2-2 draw with Malaga: "I didn't know which team Pep was going to sign for. He didn't tell me. I've read that he had a confidentiality clause.
"I don't know the possible teams that he had, or the conditions, or the squads, or how to play those teams right now.
"I'm sure that he chose by thinking a lot and it's clear that he couldn't be wrong because all the teams were great, in England and Germany. Bayern have a very good infrastructure."
Javier Mascherano was signed by Guardiola from Liverpool, and he believes the Spaniard’s choice of club was down to their homegrown selection.
He said: "I think Pep chose Bayern because of their football philosophy and because they have many German-born players."
Barca goalkeeper Jose Pinto is another to send his congratulations to Guardiola, and he admitted a European tussle could be on the cards in future seasons.
"If Pep is happy, we are happy too," he said. "If Guardiola has decided go to Bayern, we are happy for him because he wants to come back [to football]. Of course, we may even meet him in Champions League!"