Rayo Vallecano had led inside the opening minutes at the Ramón Sánchez-Pizjuán through Álvaro García, but Sevilla fought back through Jon Guridi's spot kick early in the second half before Peque's stoppage-time penalty completed the turnaround. San José, making his top-flight managerial debut, was left to reflect on fine margins.
"It's been a very hard defeat. The players made a huge effort on a very difficult pitch," he said.
Asked specifically about the penalty conceded by Florian Lejeune, San José made clear he disagreed with the decision without directly criticising the officials.
"I don't know if it is one. If they'd reviewed it I think they would have overturned it because for me there's no contact, but I'm not going to judge what they've given. They disallowed us a fantastic goal and when that happens it makes a huge difference."
The Basque coach felt his side merited more from the contest as a whole.
"It was a very intense match. Both teams struggled to find our shape at times and the football was very direct. In the second half we made a huge effort, the substitutions helped us freshen things up. The draw at the end wouldn't have been a bad result, but we felt we could even go ahead because they ended up with a man fewer because they also went to the limit."
San José was encouraged by aspects of his team's identity on show, even in defeat.
"On intensity in the high press, I think we showed it, and I liked the verticality too. We need to add more possession with the ball. We want to be a team that presses, is vertical and works for each other. I think the point would have been the fairest outcome. There are a lot of things I liked."
He also pointed to missed chances in a first half in which Rayo were the better side.
"In the first half we could have gone in with a really important advantage, we read the game well by going on the attack. That efficiency is something we've been working on. I think we're going to take a step forward because we're getting into the opposition box with ease."
Sevilla finished the match with ten men after Kike Salas was sent off late on for a heavy challenge on De Frutos, though the numerical advantage came too late for Rayo to find a winner.