Madrid, who lost to Valencia on Wednesday, were unimpressive once again and fell behind to Marc Cardona's goal six minutes before half-time at the Santiago Bernabeu.
They rallied after the break and ultimately won thanks to a Karim Benzema brace, but questions will again be asked of Los Blancos' performance.
Zidane has often been asked in recent weeks about the future of Bale and the Frenchman has done little to hush the stories claiming he wants to leave the club.
The Wales international, who has often endured a trying relationship with the Madrid faithful during his time in the Spanish capital, was jeered during the match and Zidane hardly made an impassioned defence of his player afterwards.
When asked – again – if Bale will be at the club next season, Zidane told reporters: "We'll see.
"I will not say what will happen. He's at Madrid and he has two years left on his contract. It is not the time to talk about that.
"We do not rejoice at the jeers, but the fans want their team to do better."
With Madrid realistically out of title contention in La Liga and eliminated from the Copa del Rey and Champions League, Zidane has conceded after multiple games in recent weeks that it is difficult for his side to remain fully motivated .
However, Zidane insists they will not stop fighting for results and believes the comeback against Eibar shows the squad still has the determination to finish strongly.
"In this situation, we will go out little by little, insisting on working and thinking positively," he said.
"This season we will not win anything, we already know in our heads. Playing for nothing is complicated.
"I'm not saying that we're going to quit and stop fighting. No, that's why the second half was very good, we took initiative. But thinking about the seven matches we have left, we will have to fight as a team."