Missing injured Argentina forward Lionel Messi, the champions struggled to break down a well-organised Gijon side before Daniel Alves sent Villa clear in the 49th minute and he finished clinically past goalkeeper Ivan Cuellar.
GEAR:Save yourself 10% when you get the new Barcelona shirt here with Kitbag
"It means they are in the first division and, what's more, it's a team I have been able to score against regularly," he told Spanish television.
Villa's Spain team mate Andres Iniesta had Barca's best chance of the first half but Cuellar palmed his powerful low shot away for a corner.
"It wasn't a brilliant match," Barca coach Pep Guardiola said at a news conference.
"This time we failed to go after the other team which is what you have to do with opponents who sit back and don't come after you.
"We didn't manage to get the second goal that would have allowed us to relax."
Atletico Madrid spoiled Valencia's perfect start in Wednesday's late kickoff, holding Unai Emery's side to a 1-1 draw at the Mestalla.
Atletico's teenage goalkeeper David De Gea, widely tipped as a possible future replacement for Spain keeper Iker Casillas, protected his side's lead in the second half with a series of fine saves as Valencia pressed for an equaliser.
In Wednesday's other matches, promoted Levante clinched their first win of the season after three straight defeats with a 1-0 victory at Almeria.
