Had Ronaldo scored the spot kick it would have taken him to an incredible 50 career hat-tricks.
The victory means Zinedine Zidane's defending champions have now accumulated 18 points from their last seven league games - during which they have scored 30 goals - to turn the heat up on second-placed Atletico Madrid.
Ronaldo returned to side and lined up alongside Bale and Benzema in the attack. Not necessarily because of his two goals, both of which were fine finishes, but more so the way he surrendered the chance for a hat-trick by allowing Benzema to take a late penalty.
"You build your confidence with games like this", Zidane said.
Alaves - Pacheco 7, Laguardia 5, Alexis 5, Ely 6, Duarte 5, Alfonso 5, Torres 6, Garcia 6, Perez 7, Guidetti 7, Sobrino 6. Benzema flicks a pass through to Ronaldo, with the Portuguese forward swivelling and smashing a finish into the back of the net. It just won't go in for Benzema!
The Frenchman had Ronaldo and Bale charging forwards to his right and left. His goal came 28 seconds after the restart, Real's quickest second-half goal since 2004.
"I think he has been one of the players that has turned Real Madrid around over the last couple of weeks".
Benzema had an effort disallowed for offside, Bale skimmed the crossbar with a 20-yard effort before Ronaldo made it 3-0 in the 61st minute.
Brazilian full-back Marcelo is another casualty for Real Madrid while young defender Jesus Vallejo is another absentee.
Los Blancos rounded off the scoring in the 90th minute when they were awarded a penalty which Benzema surprisingly stepped up to, making no mistake to seal a 4-0 win.
Real Madrid became the first Spanish team to score 100 goals in all competitions this season.