Ronaldo then netted the victor in the 84th minute to keep Real's slim LaLiga title hopes alive.
Zinedine Zidane, along with Real players on the bench are left surprised and confused as they see Ramos leaving.
Later on Saturday, Valencia moved back to within a point of Real and all but ended Sevilla´s hopes of finishing in the top four by beating Los Rojiblancos 2-0.
The Spain worldwide did eventually return to the field of play and, after the game, Zidane confirmed the former World Cup victor endured a bit of an embarrassing moment.
Isco's not been having a disco in 2018.
Cristiano Ronaldo's goals were his 17th and 18th in the league this season. "He went to the bathroom".More news: Philips introduces its first outdoor Hue lights
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Overlooked for Real's two biggest games of the season so far, the indication is Zidane does not trust Bale when it matters most.
Eventually Madrid appeared to exert a degree of control and Ronaldo - following a moment of Luka Modric inspiration - opened the scoring in the 34th minute, continuing his brilliant recent form. After the home side equalised the score after halftime, the Portuguese goal machine came from behind and rescued three crucial points for Zinedine Zidane's men. But he was running really well, if not faster than normal, so something seemed fishy. Today we had difficulties with the ball, technically we made a lot of mistakes in our passing, playing out from the back. The 31-year-old reappeared to finish the game but the question remained, where did he go?
But for Ronaldo's clinical instincts in front of goal, that slip-up should have proved costly and Eibar deserved something from a match in which they poured their heart and soul into.
Rodrigo Moreno netted his 11th and 12th league goals of the season.
Off day: Whites captain Sergio Ramos.