The 36-year-old - only starting in Russia after Sergio Romero withdrew from the squad due to a knee injury - gifted Ante Rebic a 53rd-minute goal after a woeful attempted pass lacked the power to evade the forward.
That set in motion a painful second half for Argentina, who conceded further goals from Luka Modric and Ivan Rakitic to leave them in danger of needing a win and a swing in goal difference in their final Group D game against Nigeria to reach the last 16.
Sampaoli was quick to shield Caballero from inevitable criticism, suggesting it was his own preparation for the game that was to blame.
"I was very hopeful and I have a lot of pain because of the defeat, I probably did not read the game properly," he said.
"You are right, I am the one to make the final decision on these things.
"The key to the defeat relates to my responsibility because I'm the coach. I had to devise a plan, had I set up differently things might have worked out better. I don't think it's realistic to put the burden on Caballero."
Argentina will have a clearer idea of what they need to do in their final game after Friday's other Group D clash between Iceland and Nigeria.
Despite the shattering loss to Croatia, Sampaoli is adamant his side have not given up their pursuit of a spot in the knockout rounds.
"We were very excited before this game, to be able to get the first place and be close to the qualification," he added.
"This moves us away and makes it very painful for everyone.
"Now we have to fight to achieve a place in the next phase."