The Catalan team scored two goals in the last quarter-hour of the match through its players Andres Christensen and Marcus Rashford in the 76th and 90th minutes.
Barcelona qualified for the round of 16, joining Deportivo La Coruna, Elche, Real Sociedad and Valencia, which advanced at the expense of Mallorca, Eibar, Eldense and Sporting Gijon earlier on Tuesday evening.
The match was postponed from its original date for half an hour by a decision of the security authorities due to a problem related to the entry of fans into the stands of the Pedro Escarten Stadium, which has a capacity of 8,000 spectators.
Barcelona coach Hansi Flick took advantage of the large technical differences between him and his competitor, who plays in the Spanish third division, to give an opportunity to a large number of substitutes, young players, and those returning from injury.
German goalkeeper, Marc-Andre ter Stegen, participated for the first time this season after recovering from a back injury that kept him out since the preparation period.
Flick had announced that Ter Stegen, Barcelona’s captain, would be the team’s third goalkeeper behind Joan Garcia, who recently joined this season, and Polish Wojciech Szczesny, who will return from retirement in the summer of 2024.
Flick also included the young quartet of Marc Casado, Marc Bernal, Joffrey Torrents and Ronnie Bardagi.
The hosts almost scored with an early goal, but Ter Stegen was alert in saving Barcelona’s goal by blocking Manu Ramirez’s shot in the fifth minute, and Caniso shot a ball near the post in the 15th minute.
Guadalajara withstood Barcelona and left with a clean sheet in the first half thanks to the brilliance of its goalkeeper, Dani Vicente, who blocked a number of attempts from Eric Garcia, Christensen and Rashford.
Lamine Yamal, Paradji and Fermin Lopez also missed other attacking attempts for the guests, so the first half ended in a goalless draw.
The Guadalajara goalkeeper continued his brilliance in the second half, blocking three new attempts from Rashford and Bardaji.
Ter Stegen was subjected to no less serious tests with shots from Danielle Gallardo and Tony Calvo, before Christensen opened the score with a goal with a header after a perfect cross from Frenkie de Jong.
A few minutes after Barcelona’s goal, Ter Stegen blocked a powerful shot from Salivo Karubici, before the Catalan giant confirmed its superiority with a second goal scored by Rashford in the 90th minute after dribbling the goalkeeper, taking advantage of a perfect through ball by his teammate Lamine Yamal.
