Carlo Ancelotti's men were not quite at their best as they welcomed their Madrid neighbours, but they rarely looked like dropping points in an ultimately comfortable win.
It took the hosts less than 10 minutes to break the deadlock as Gareth Bale grabbed his first goal in five Madrid games and, although Sergio Ramos doubled the lead just before the break, former Real youngster Alberto Bueno scored to ensure Rayo were just one behind at half-time.
But the Italian's decision was vindicated just nine minutes in, with Bale getting on the end of Kroos' teasing delivery to give Real an early lead.
The hosts struggled to build on that early goal, though, and they had Keylor Navas - in for Iker Casillas - to thank for keeping them ahead in the 21st minute as he palmed away Leo Baptistao's stinging drive.
Rayo's resurgence almost fell apart a few moments later, but Mohammed Fatau escaped punishment despite seemingly bringing Ronaldo down when through on goal.
But Real eventually doubled their lead in the 40th minute as James Rodriguez's corner was flicked on by Pepe and Ramos - attempting a volley - diverted the ball home with his thigh.
Rayo did hit back with a goal of their own shortly after, though, as Baptistao pounced on Rodriguez's dreadful back-pass before squaring to Bueno for an easy finish.
Goalkeeper Cristian Alvarez tipped Bale's fierce volley on to the crossbar, but he gifted Real a fifth moments later, allowing a tame Ronaldo effort to squeeze between his legs to give the scoreline a resounding look.
