Sergio Camello had given the hosts the lead before Mariano Diaz capitalised on a defensive error late on to rescue a point for the visitors, in a match forced to be played away from Vallecas after the Community of Madrid withdrew the stadium's licence for renovation work.
Head coach Beñat San José spoke to reporters afterwards about his side's performance, Batalla's injury and the lack of a home crowd.
"We've had a very good, very complete match," San José said. "We played very vertical football in which we showed all our qualities against a very difficult opponent. The players were dynamic. Today they ruled out another goal of ours, we accept it and that's it.
"The other side was that their goal came from an unfortunate action of ours, and the forced changes. You stop having two changes at the moment you want to have them, plus the last window, it has cost us in the final fifteen minutes. I think we should have taken all three points."
On Batalla's injury, which forced an unplanned reshuffle, San José added: "It stopped us being able to change the play from side to side. It was a very disrupted match. We have to assess when we've had everyone available. Batalla was with the doctor and I still hadn't been given any report."
Alavés head coach Quique Sanchez Flores struck a similarly frustrated tone despite the point, pointing to his side's ability to respond after falling behind.
"We haven't taken their goal well," Sanchez Flores said. "We felt bad because we didn't deserve it. The match led us into that situation through a moment of brilliance from Camello, and we recovered our sense of the game after a few minutes.
"The team imposed itself, went forward, we changed the system and the players reacted well. The players are angry because we don't settle for a draw away from home."
Sanchez Flores also praised the performance of Mariano, whose goal salvaged the point.
"He has to do two things in attack and two things in defence," he said. "He has to devour what's in front of him and go into every match doing the things that are fully asked of him. I love that the goal came from an advanced press with faith in it."
San José, for his part, was keen to stress that the sparse crowd at Butarque, with many Rayo Vallecano fans staying away in protest at the enforced ground-share, should not be used as an excuse.
"I've never put forward any excuse, but this point is huge," San José said. "Thank you from the heart to those who came, and I feel sorry for those who didn't, but we understand them completely. It's a real blow. It's a triple effort that we all have to make.
"But we're not going to lead with the excuse. Imagining Vallecas full is an extra boost of energy, and I ask that the next match be played at Vallecas."