Madrid had won three of their four matches under Zinedine Zidane ahead of this short trip south, but they struggled for invention and had to battle back from a goal down for the fourth game running.
Benzema struck early in the second half to cancel out Jonathan Silva's opener through the final meaningful kick of the first half, making it a combined 10 goals and assists in the Frenchman's last six outings.
There was to be no winner for the visitors, however, meaning that they dropped points against their Madrilean rivals for the first time in the league.
Leganes defeated their neighbours here in a Copa del Rey tie earlier this year, and they showed once again why they have been so difficult to beat on home soil this term.
Madrid struggled to create many goalscoring opportunities in the first half, the best of which fell to Marco Asensio in the opening 10 minutes.
The home side were more than holding their own, coming close to a breakthrough when Dimitrios Siovas outjumped Dani Carvajal to set up Martin Braithwaite for a close-range header, which the striker could only send wide once getting in front of Nacho.
Leganes then had a couple of weak penalty shouts rejected, including one for a slight shove from Carvajal on Braithwaite when defending a corner.
Right at the end of the first half, just after Raphael Varane had a rare shot kept out by Cuellar from a Benzema knockdown, Silva gave Leganes a surprise lead.
Madrid required just six minutes of the second half to level up the contest, though, doing so through a Benzema strike.
Luka Modric turned on the edge of he box, played in his teammate and the in-form striker converted past Cuellar from the edge of the six-yard box after his first shot was brilliantly kept out.
Leganes offered a good response, with Silva arriving late in the box and guiding Allan Nyom's cross wide, while Asensio's front-post flick was stopped by Cuellar soon after at the other end of the pitch.
Another decent opportunity came and went for Asensio, who tried and failed to flick the ball over Cuellar at his near post, and the Leganes keeper did well to keep out a powerful strike from Marcelo as the game entered its final 10 minutes.
Mauricio Pellegrino's men thought they had snatched a first league win over their opponents at the sixth attempt late on when Youssef En-Nesyri latched on to Nyom's through-ball and slotted it past Navas, but the offside flag rightly cut his celebrations short.
Zidane chucked on Gareth Bale for the closing stages of the game, but the European champions lacked ideas and in the end a point apiece was the right outcome.
LEGANES (5-3-2): Cuellar; Nyom, Bustinza, Omeruo, Siovas, Silva; Vesga (Recio 71'), Perez, Eraso (El Zhar 71'); Carrillo (En-Nesyri 65'), Braithwaite
REAL MADRID (4-3-3): Navas; Carvajal, Varane, Nacho, Marcelo; Valverde, Casemiro, Modric; Isco (Vazquez 77'), Benzema, Asensio (Bale 81')