The deadlock was broken on 34 minutes as Luka Modric played a sublime long pass to Ronaldo, who fired home at the near post from 12-yards out.
Former Wigan defender Ivan Ramis headed in an equaliser for Eibar and it looked like they would secure a point.
But it was right back Dani Carvajal who intercepted a pass by Leon and crossed for Ronaldo to head in his second goal with six minutes remaining.
The Portuguese forward now has 14 league goals in his last eight matches and has scored in each of his last seven games in all competitions, netting 13 in total in that sequence.
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The spokesperson for the Health Ministry, Wahid Majro, said several of the wounded were in critical condition and he feared the death toll could rise further.
"They were better. They played a great game", Zidane said.
But Ronaldo proved the difference again, the 33-year-old taking his tally for the season to 35 goals in 37 appearances.
In front, Real improved but five minutes into the second half and Eibar were level.
However, when his French manager was asked about his player's absence following Cristiano Ronaldo's late victor, the former midfielder was only too happy to explain the somewhat vomiting-inducing reason behind it.
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An event in Toronto will honour Prime Minister Justin Trudeau for his work in promoting gender equality . Barbados and the Caribbean can be justifiably proud of the achievements of its girls and women.
Isco saw a 23rd minute shot blocked inside the Eibar box, but after Joan Jordan saw his header from a Pedro Leon free-kick fly just wide of the target, Real found themselves in the lead, very much against the run of play. Subs: Nacho Fernandez (for Varane, 28) 5, Karim Benzema (for Kroos, 71) 5, Lucas Vasquez (for Isco, 71) 6.
The hosts were in a confident mood as they pegged their opponents back in their own half early on, with Kike twice close to connecting to threatening crosses from Takashi Inui.
Ronaldo put Madrid ahead in the 34th minute after Luka Modric intercepted a ball from defender Aritz Arbilla and placed a flawless pass for the Portugal forward to control with his chest and fire in.
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Fittingly, he will likely lose the album after being order to forfeit $7.36 million in assets. Some of his supporters sent letters asking Matsumoto not to lay down a harsh sentence.