Enrique made seven changes to the side that beat Real Betis 6-2 in the champions' previous fixture, with Lionel Messi, Luis Suarez and Andres Iniesta used as substitutes.
"I am the one ultimately responsible for all the bad things that happen," said Enrique.
The result was Enrique's fifth home loss in two seasons as Barca manager.
Alaves' win, secured by Ibai Gomez's goal after Jeremy Mathieu had equalised for Barcelona just after half-time, was their first in the league at the Nou Camp since 2000.
The defeat came three days before Barcelona host Celtic in their opening Champions League group game on Tuesday night.
"Many of the changes came from the circumstances surrounding us, but we have 22 players and we are going to use everyone this season," added Enrique.
"We lacked fluidity, precision and we were fragile in defence, which is one of the things that normally makes us strong."
Messi and Suarez were among a number of Barcelona players to have been away on World Cup qualifying duty before the game, while Enrique gave debuts to former Ajax goalkeeper Jasper Cillessen and striker Paco Alcacer, who signed from Valencia in August.
Barcelona coach Luis Enrique accepted the blame for Barcelona's shock 2-1 La Liga defeat by newly promoted Alaves.