With just two minutes remaining Gareth Bale was brought down in the box and the referee awarded the penalty.
Having heard his team-mate jeered earlier in the contest, the Portugal worldwide then selflessly let Benzema convert an 89th-minute penalty after Victor Laguardia brought down a marauding Bale.
"Cristiano's gesture speaks volumes for the type of team this is and how he is as a person", goalkeeper Navas said post-match. However, Madrid's regular penalty taker who was also on a hat-trick made a decision to hand over the duty to Karim Benzema who after all his efforts had yet to get on the score sheet. A brace from Ronaldo and goals from Bale and Benzema saw the match through quite comfortably.
Benzema set up Ronaldo's opening goal against Alaves with a stylish backheel and the first thing Real's all-time top scorer did after finding the net was to point towards Benzema, appearing to ask the supporters to show him more respect. "Karim deserved this, to score a goal, as he had played a very good game".
However, Real's regular penalty-taker instead gave Benzema the chance to net for only the fourth time in La Liga this season and potentially ease some of the pressure on his head.
Gareth Bale won a late penalty which Karim Benzema scored from
"I wanted to see him in that position and now we see how we play in the upcoming games", coach Zinedine Zidane said. Manager Fernandez is likely to continue with the 4-4-2 setup at the Bernabeu, but there will be changes expected from the side that beat Deportivo La Coruna 1-0 in their previous game.
With Alaves giving as good as they got on the counter-attack - Alfonso Pedraza and Alexis both drew vital saves out of Keylor Navas in the first half - Madrid knew an 11th victory in their last 12 meetings with the Basque side was far from certain. That went well for us. "Maybe we needed a game like this".
Alaves come into the game high on confidence, having won three back to back games in the La Liga.
Real have a kinder schedule than Atletico between now and the worldwide break which begins on March 19, with Simeone's side visiting Barca a week after their game with Sevilla, while Zidane's side face Espanyol away after the Alaves game followed by a home game against Getafe.