The Cup holders left several big names including Neymar and Luis Suarez at home and produced few chances on a difficult pitch against a charged up Villanovense, who were backed by a vociferous 10,000-strong home crowd.
Barca will be confident of finishing off the tie in the second leg at the Camp Nou on Dec 2.
"We are happy not to have conceded a goal and it was a solid performance from us," Barca keeper Jordi Masip told reporters.
"The pitch influenced the game as they were tough conditions."
Wilfrid Kaptoum made his debut, with Barca coach Luis Enrique playing several youth team players alongside squad members.
Villanovense harried the visitors and Pablo Moraga had the first shot of the game with his drive from the edge of the area going wide after seven minutes.
The team from the small town of Villanueva de la Serena in the west of Spain defended resolutely, intending to pounce on the counter against a Barca side that found it difficult to play their usual passing game.
Munir El Haddadi did have a clear sight of goal on the half hour but fired over and at the other end Javi Sanchez flicked a corner kick just wide with an outstretched leg.
A vicious Sandro Ramirez strike later went narrowly wide and a header by Marc Bartra from a corner was tipped over by home keeper Jose Antonio Fuentes.
(editing by Clare Lovell)
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