David Mainz slotted in from close range in the second half to give the Segunda Division B side a shock lead.
But teenager Carles Alena drilled in from outside the box to level for Barca, who were without star forwards Lionel Messi, Luis Suarez and Neymar.
Barcelona next face arch rivals Real Madrid in La Liga on Saturday.
The champions will go into El Clasico (kick-off 15:15 GMT) in second place in the table, six points behind Zinedine Zidane's leaders.
Luis Enrique's Barca side have now drawn their last three domestic matches, following league draws with Malaga and Real Sociedad.
The second leg against Hercules takes place at the Nou Camp in three weeks' time on Wednesday, 21 December.
Meanwhile, Atletico Madrid thrashed third-tier side Guijuelo 6-0 in their first leg tie, with Yannick Ferreira-Carrasco scoring twice for Diego Simeone's side.
Imagine you could pick from the combined squads of Barcelona and Real Madrid - tasty but testing. Who would you choose?
Holders Barcelona were held to a draw at third-tier side Hercules in the first leg of their Copa del Rey last-32 tie on Wednesday.