The Portuguese former World Player of the Year smashed in a trademark swerving free-kick in the 22nd minute at the Madrigal and followed up with a similar effort in second-half stoppage time to complete a 3-1 victory.
His second of the night equalled the record jointly held by former Real striker Hugo Sanchez (1989/90) and former Athletic Bilbao forward Telmo Zarraonandia, known as Zarra (1950/51).
"The run I am on is good, not for me but for the team, because scoring so many goals is very good for everyone," Ronaldo, who has netted nine goals in his last three matches, said.
"I am pleased on a personal level, although not completely because we wanted to win the league and the Champions League," the 26-year-old former Manchester United player added.
Ronaldo has scored 51 in all competitions this season, including six in the Champions League and seven in the Copa del Rey, and can set a league record with a goal in Real's final match of the season at home to Almeria next weekend.
Neat finish: Cristiano Ronaldo from Portugal, center, scores past Almeria's goalkeeper Esteban Andres Suarez
Record breaker: Real Madrid's Cristiano Ronaldo, right celebrates his strike with Pepe, left and Karim Benzema
Real Madrid star Cristiano Ronaldo tonight broke the Primera Division record for goals in a single season after netting his 39th of the campaign against Almeria.
Ronaldo needed just five minutes of Madrid's final game of the season against already-relegated Almeria to seal his place in the record books.
Xabi Alonso's free-kick to the far post was headed back across goal by Sergio Ramos and the unmarked Ronaldo was on hand to poke in the opening goal of the game.
That strike saw Ronaldo move one clear of the previous all-time record, which he jointly held with Madrid's Hugo Sanchez, from the 1989/90 season, and the legendary Athletic Bilbao striker Telmo Zarra, who achieved the feat during the 1959/60 campaign.
Ronaldo, who had scored nine goals in his previous three games heading into the fixture, has now netted 52 in all competitions for Madrid this season.
even this doesn't happen in my fm game...
Ronaldo should have a real hard look at himself and wonder why those goals don't come in the big games on a regular basis. He looked terribly average when he played against barca this season.
COME BACK WHEN U HAVE WON 19