The 31-year-old striker, who debuted for Real in October 1994, netted the opener in Soria after Juan Pablo Colinas could only parry Gonzalo Higuain's shot early in the second half.
Arjen Robben, who had helped set up Raul's opener, bagged the second soon after, cutting in off the right flank to shoot from the edge of the area.
Real's sixth successive win strengthened their hold on second place with 44 points, but they are still nine short of leaders Barcelona who visit Racing Santander on Sunday.
"Di Stefano was one of the greatest players there has been so to equal his goal-scoring record says everything," Real coach Juande Ramos said of Raul's achievement.
"He brings a lot to the team and scored the first goal tonight which was crucial to helping us to win the game."
Numancia's Javier del Pino headed against the post as the home side kept Real at bay in a chilly first half, with Robben closely marshalled.
Three minutes into the second period, however, it was Robben's run that created the opening for Raul to slot in Gonzalo Higuain's parried shot.
Malaga stay seventh with 32 points, three ahead of ninth-placed Bilbao, who travel to Sevilla in the first leg of their King's Cup semi-final on Wednesday.
RATE: Individual player performaces from ALL this weekend's La Liga fixtures on Talentspotter
