Ronaldo struck either side of Gareth Bale's strike 28 seconds into the second half, while Benzema recovered from an abject start to the match by assisting Los Blancos' first two goals.
Having heard his team-mate jeered earlier in the contest, the Portugal international then selflessly let Benzema convert an 89th-minute penalty after Victor Laguardia brought down a marauding Bale.
The result means Madrid have won five consecutive matches in all competitions for the first time this season and Zinedine Zidane will draw particular encouragement from his headline attacking stars operating so brilliantly in tandem.
A fourth consecutive LaLiga victory was ultimately too much to ask for a resurgent Alaves, who showed plenty more of the their encouraging form under Abelardo before being outgunned, Galactico-style.
Alaves should have been behind in the 18th minute when Mateo Kovacic and Theo Hernandez orchestrated a lightning counter-attack, but the much-maligned Benzema lost his footing to skew wastefully wide and draw whistles from a section of the Madrid faithful.
Benzema proved a more effective provider in the hosts' next attack of note, skipping around Alexis and crossing for Bale to send a spectacular overhead kick just wide.
The visitors grew into the game and Madrid goalkeeper Keylor Navas reacted sharply to thwart Alfonso Pedraza low down to his left.
Bale failed to punish a poor clearance from Navas' opposite number Fernando Pacheco at the other end, but Madrid led in the 44th minute.
After collecting a cute backheel from Benzema, Ronaldo turned to produced an assured left-footed finish and the five-time Ballon d'Or winner gestured towards his team-mate during the celebrations, seemingly asking for the crowd to show some appreciation.
Benzema did indeed receive some warm cheers when he cut inside to fizz a shot over in first-half stoppage time, an attempt that came after Madrid failed to clear a corner and Navas patted away an Alexis strike at his near post.
Alexis was culpable in a nightmare start to the second half for Alaves, Benzema snapping the ball off his toes.
The Frenchman had Ronaldo and Bale charging forwards to his right and left. He elected to pick out Bale, who vindicated the decision by clipping a low shot past Pacheco.
Madrid began slicing Alaves open at will and it was a surprise of sorts that it took until the 61st minute for goal number three to arrive.
Bale swept a pass out to Lucas Vazquez on the right and Ronaldo timed his run perfectly to convert the Spain winger's low cross for his 28th goal of the season.
Lucas thrashed into the side-netting and was again denied the goal his efforts deserved 15 minutes from time, this time by the impressive Pacheco.
Ronaldo's no-look pass to Lucas was the sign of a man basking in a buoyant Bernabeu atmosphere and he judged the mood perfectly when he let Benzema arrow a spot-kick into the bottom-left corner and crown a redemptive outing.
