Luis Suarez put the Atletico ahead inside the first quarter of an hour with a deft finish while the hosts spurned several further chances as they looked to consolidate their position ahead of second-placed Barcelona.
Real, who had penalty claims waved away despite Felipe's apparent handball, rallied in the closing stages and although Benzema was twice denied by Jan Oblak, he finished a fine move with two minutes to go.
Atletico moved three points clear of Barca while they remain five ahead of Real – although they have a game in hand on both their rivals – after their late misfortune on a day where Kieran Trippier returned to the ranks after a 10-week betting ban.
Tripper started the move that led to Atletico's opener after 14 minutes, passing upfield to Marcos Llorente, who skipped past Nacho before putting Suarez clean through and the Uruguayan produced a finish of the highest order.
Suarez looked up and, with the outside of his right boot, skilfully swerved the ball beyond the onrushing former Atletico goalkeeper Thibaut Courtois as the hosts hit the front following an uneventful opening few minutes.
Yannick Carrasco was just unable to connect with a cross from Suarez, who was a constant thorn in Real's side throughout although Courtois was able to save a well-directed volley a little later in the half.
Real pleaded for a penalty just before half-time as Felipe appeared to handle in the area after a corner but nothing was given after referee Alejandro Hernandez watched several replays of the incident.
Atletico continued to hold the upper hand after half-time, with Courtois keeping the visitors within one goal as he saved well from Carrasco before denying Suarez again, smothering an effort from close range.
Joao Felix teed up Suarez shortly after being brought on but the former Barcelona striker shot straight at Courtois while at the other end Oblak was tested by a shot from distance by Real substitute Federico Valverde.
Real started to step up their intensity in the final quarter of an hour, with Oblak making a fantastic double save to thwart Benzema although the Frenchman pounced two minutes from time to ensure a share of the spoils.
After Atletico sloppily gave away possession, Benzema coolly played the ball to Casemiro and carried on his run before slotting in an empty net after collecting a return pass from the Brazilian.