Ronaldo had scored a hat-trick in the 7-3 mauling of Sevilla on Wednesday and the Portuguese took just three minutes to open the scoring with a cool finish after racing onto Luka Modric's pass.
Rayo then had a strong penalty appeal waved away and a goal disallowed, but Madrid doubled their advantage just after the half hour mark as Bale's right-footed cross picked out Benzema to nod home his seventh goal of the season.
Ronaldo added a third just after the interval from Bale's low cross, but two Jonathan Viera penalties in as many minutes gave Rayo hope.
The hosts then piled on the pressure for the final half hour and Alberto Bueno struck the post as they came agonisingly close to an incredible comeback.
And despite holding on for the win, Real boss Carlo Ancelotti was furious with his side's lack of control after half-time.
"Against Sevilla we were 3-0 up and let them back into the game. Today the same thing happened and that is not a coincidence," he said.
"We need to change and remove the superficiality we have on the pitch, the second-half was a disaster. You cannot let a team back into the game like that when you have the quality of Real Madrid."
Bale was starting a second consecutive game for the first time in his Madrid career and Real started where they left off in midweek as Ronaldo took advantage of Rayo's dangerous high line to skip past Alejandro Galvez and slot calmly past the keeper for his 19th goal of the season..
Rayo were very unfortunate not to be awarded a penalty moments later when Dani Carvajal appeared to clip Nacho inside the area.
The hosts did have the ball in the net on the half hour mark when Iago Falque turned Lass Bangoura's cross towards goal, but the ball struck Viera on its way into the net and was rightly ruled out for offside.
Within two minutes of that let off, Madrid had made it 2-0 when Bale raced clear on the right and his measured cross was headed home at the far post by Benzema.
Real could have extended their lead before half-time as they continued to pick off Rayo on the counter-attack and Ronaldo lashed an ambitious volley over before flicking a header wide of the far post.
Ronaldo looked to have wrapped up the points when he prodded into an open goal from Bale's inviting cut-back four minutes after the break.
However, Rayo were back in the game when Viera converted his first spot-kick after he had been brought down by Pepe.
Joaquin Larrivey then struck the bar with a diving header, but as the ball ricocheted around the area from the rebound Bueno was brought down by Marcelo for a second penalty.
Viera stepped up again and his strike had just enough power to beat Lopez despite going the right way.
Bueno then thrashed a shot against the post and pulled another effort inches wide as Rayo forced Madrid onto the back foot for the majority of the second period.
However, on a rare Madrid breakaway, Ruben Martinez made a brilliant double stop to deny Ronaldo his hat-trick.
Right-back Tito had one final chance to snatch a famous point for Rayo deep into stoppage time, but his header floated just wide as despite a brave effort an ninth defeat of the season sees them drop to the bottom of the table.
Elsewhere in La Liga, Real Sociedad thrashed Osasuna 5-0 at home with five different goalscorers. Almeria defeated Real Valladolid thanks to a lone goal from Rodri, while Sevilla lost at home to Celta Vigo from an Alex Lopez goal.