Carles Alena, Borja Lopez and Alejandro Carbonell were all handed their first-team debuts for Barcelona, while Jasper Cillessen, Aleix Vidal and Paco Alcacer were also among the starters in a much-changed team.
The Spanish champions had to wait until the 11th minute to register a shot on target via a deflected Alcacer free kick, but Hercules goalkeeper Ivan Buigues was on hand to make a smart save.
Hercules, despite conceding the possession, were a threat on the counter-attack in the opening 45 minutes and Manuel Gaspar tested Cillessen on the half-hour mark after driving past Lucas Digne, before Cameroonian midfielder Emmanuel Omgba fired into the stands after spotting Cillessen off his line.
Lopez had Barcelona's next serious chance in the 36th minute after meeting a deep free kick from Denis Suarez, but the Barcelona B centre-back cleared the target with his effort as Hercules kept their first-half clean sheet intact.
Gaspar tested Cillessen with a free kick early in the second period as Hercules continued to impress, and the home side had a shock lead in the 52nd minute when centre-forward David Mainz chested a Alvaro Salinas cross into the back of the net from close range.
Barcelona were on terms just six minutes later, however, when debutant Alena found the bottom corner with a strike from outside the home side's box.
Another Barcelona debutant Marc Cardona, who replaced Alena, came close to scoring a second for the holders 10 minutes from time, but Buigues was on hand to make a smart save as it finished level ahead of the second leg next month.