Ronaldo converted Toni Kroos' pass, but Cristhian Stuani's header made it 1-1.
Real retook the lead with a powerful strike from Ronaldo and he then set up Lucas Vazquez for the hosts' third before completing his hat-trick.
Stuani headed in Girona's second, Gareth Bale scored Real's fifth, Juanpe pulled one back but Ronaldo got his fourth and Real's sixth in injury time.
The result takes Real, Spanish champions last season, above Valencia but they are still four points behind city rivals Atletico, who fell to a surprise 2-1 loss at Villarreal.
Real are still 15 points behind leaders Barcelona, who won 2-0 at home to Athletic Bilbao earlier on Sunday.
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