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.
Third-placed Sevilla, on 38 points, travel to Sporting Gijon 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.
PULSATING ENCOUNTER
With Numancia still reeling, Robben raced through to score the second in the 56th and the visitors comfortably maintained their advantage, despite Fernando Gago being sent off for picking up his second yellow card near the end.
Earlier, Athletic Bilbao came from behind to beat Malaga 3-2 in a pulsating encounter at San Mames.
Promoted Malaga twice took the lead through Albert Luque and Lolo and were close to breaking into the Champions League places.
In-form striker Fernando Llorente set up the first Bilbao equaliser for Fran Yeste just before the break.
Llorente then powered in a spectacular goal in the 71st minute before Markel Susaeta rose to head the winner four minutes from time.
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
