The 29-year-old was left out of Barca's starting XI for the fourth game in a row on Saturday as Pep Guardiola opted for an attacking trio of Lionel Messi, Alexis Sanchez and Isaac Cuenca.
Villa came off the bench in the 67th minute to score Barca's fourth goal, and Guardiola was made to explain his decision not to give the Spaniard more playing time in recent matches.
"When I tell you that I have a lot of trust and faith in Villa, I mean it," Guardiola told a post-match conference.
"Thiago did not start either and he has been playing at a very high level, and neither did Andres [Iniesta].
"I cannot justify every time he has been a substitute. Not everyone can play, but I trust everyone. I know every player and what they can bring to the fare."
Guardiola went on to praise Lionel Messi, who turned in another great display and scored Barca's second goal.
"Messi does not complain, nor does he fall to the ground, if he does not feel pain," Guardiola enthused, after the Argentine had visibly been in pain after suffering a challenge during the game.
"I was worried, but he said he was fine so I decided that he should continue. He gives us many things as he can unbalance the game."