Real were missing three of their first-choice defenders as captain Sergio Ramos and Dani Carvajal were suspended and Marcelo was injured, but they eased past visiting Alaves for an eighth win in a row.
The struggling visitors still managed to cause plenty of problems for Real's makeshift defence after going behind, with Scottish winger Oliver Burke forcing Thibaut Courtois into a good save and later teeing up Joselu, whose shot ballooned over the bar.
Real doubled their lead soon after half-time when Benzema picked up a through ball and squared to Marcos Asensio for an easy tap in that was confirmed by VAR after a review for offside.
VAR also worked in their favour for the penalty, following a week in which Barca's president and coach raged against how the technology has been used recently.
"The noise about VAR does not bother us, we can only control the attitude we continue to show on the pitch," said Real defender Raphael Varane.
"We are focused on our objective and we have three finals left. It was vital to win and it was important to keep another clean sheet and that gives us a lot of confidence."
Madrid continued to dominate proceedings, but had nothing more to show for it as the match ended 2-0.
The result puts Real Madrid on 80 points -- four ahead of Barcelona -- with three games left to play in the season, meaning Zinedine Zidane's side cannot be caught by their La Liga rivals unless they drop points.
Alaves remain in 17th place -- three points ahead of Mallorca -- as they seek to avoid relegation.
Information from Reuters was used in this story.