The Blaugrana coach has dispelled talk of a dispute between the pair and instead opted to focus on his side's perfect start to the season
The Catalan side were frustrated for large periods of the game and that appeared to boil over when Villa engaged in a heated debate with his team-mate after Messi failed to pass him the ball.
"There is nothing to gather [from what happened between Villa and Messi]," Vilanova stated at his post-match press conference.
"Whoever plays football knows discussions are a normality, and part of the game."
"Such occurrences are common signs that a team is alive. Not exchanging views for betterment would honestly suggest worse."
Messi also appeared on Barca TV to refute suggestions of a bust-up: "Do not look for problems where there are none. Villa and I get along very well, it was just normal banter during games."
Barca's fifth league victory in a row, courtesy of a late Xavi strike and Borja Gomez own-goal, puts the Blaugrana a massive 11 points clear of reigning Liga champions Real Madrid, although Jose Mourinho's outfit are due to face Rayo Vallecano on Sunday.
"What was important was to make it 15 points out of 15," Vilanova continued.
"I don't feel pressure, or any obligations. I knew what would be asked of me from the start, and I dared to try my hand."
"The key tonight was scoring the first goal, which helped open up their side. We put in a great performance tonight nevertheless."