Ronaldo recovered from a terrible start after blasting his first penalty of the day over the bar to put Madrid in front from another spot-kick just before half-time.
Bruma levelled for an injury-hit Sociedad minutes after the break, but Ronaldo delivered when his side needed a goal once more to restore the lead 23 minutes from time before Lucas Vasquez added a late third.
"Apart from 10 minutes when they were in command, we controlled the game and had a lot of chances, which, if we had taken them, would have made the second-half more comfortable," said Benitez.
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"The team reacted brilliantly (to the equaliser).
"I congratulate the players for their attitude from start to finish. We worked hard, reacted well and got the three points."
Rumours over Benitez's future refuse to go away after a disappointing first six months in charge at the Bernabeu with the former Liverpool boss even claiming there is a media conspiracy against him on Tuesday.
However, Madrid had hit 22 goals in their previous three games at home and were only denied another flying start by a hat-trick of brilliant saves from Geronimo Rulli.
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The Argentine 'keeper tipped over Pepe's looping header before showing great reflexes to deny Ronaldo and Karim Benzema from close range.
Sociedad's luck seemed completely out in the first-half, though, as they lost top-scorer Imanol Agirretxe and playmaker Sergio Canales to injury and saw referee Jose Luis Gonzalez award Madrid two controversial penalties.
The first spot-kick was given for an apparent push by Yuri Beriche on Benzema at the back post.
Yet, for the first time in his Madrid career, Ronaldo failed to even hit the target from the spot as he blasted wildly over.
The World Player of the Year made amends three minutes before half-time when he converted his second penalty after Yuri was again penalised for blocking Gareth Bale's cross with an outstretched hand.
Despite the adversity they faced, Sociedad kept the ball off Madrid for long spells and hauled themselves level in spectacular style four minutes after the break when Bruma curled home his first league goal for the club into the top corner.
The Portuguese winger then had a huge chance to put Sociedad in front moments later, but a heavy touch allowed Navas to once again scamper from his goal to make a crucial save.
Benitez's popularity with the home fans wasn't helped by his decision to replace James Rodriguez with Mateo Kovacic on the hour mark and later Benzema for Vazquez.
Yet, despite all their troubles, Ronaldo remains ever reliable source of goals and he delivered once more with a sweetly struck volley from Marcelo's corner for his 25th goal of the season.
Benitez's men had to withstand some late Sociedad pressure as Ruben Pardo's deflected effort trickled just wide.
However, Vazquez ensured all three points when he coolly controlled and finished Bale's fine cross to make it 3-1 three minutes from time.
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