Ramos spent nine years with Sevilla before moving to Real Madrid in 2005, but the Spain international was the subject of a number of cruel chants from the home supporters on the night.
Zidane has said that neither he nor Ramos was pleased with what occurred in Seville, but has admitted that such situations are 'difficult to avoid'.
"Booing for Ramos? I can't be happy with that and neither can he, but we can't avoid it. He didn't do anything important, he played his game, he's not happy because he used to play here, he's from here, and he's certainly hurt by it," Zidane told reporters.
"Now we have to be aware that these things can happen and I'm not happy for his family either."
Ramos scored a late penalty for Real Madrid as the two teams played out a 3-3 draw, which booked Los Blancos' spot in the quarter-finals of the Copa del Rey and set a new Spanish record of 40 games unbeaten in all competitions.