France striker Benzema was earlier denied several times by keeper Jan Oblak at the Wanda Metropolitano.
Luis Suarez scored the opener, which Kieran Trippier helped create on his return from a 10-week ban for betting.
Atletico are three points clear of Barcelona and five ahead of third-placed Real.
England right-back Trippier, who was suspended in December and fined £70,000 after a Football Association panel found he broke betting rules, was bright throughout for the hosts.
He started the move for Atletico’s goal, finding Marcos Llorente with a clever pass from defence.
A fine first touch from the Spanish midfielder helped him race clear before he slid the ball to Suarez, who beat Thibaut Courtois with a well-placed shot with the outside of his boot.
Real were denied a penalty for handball before the break, with referee Alejandro Hernandez watching several replays before deciding against awarding a spot-kick after the ball appeared to strike Felipe’s arm.
Courtois made a string of crucial saves after the break, denying Yannick Carrasco and twice keeping Suarez out.
At the other end Oblak made an excellent double save from Benzema with 10 minutes remaining, but Benzema could not be denied the equaliser after neatly exchanging passes with Casemiro in the penalty area.
‘Real still alive in title race’ – what they said
Atletico Madrid manager Diego Simeone said: “It depends which way you look at it. In the negative, they equalised in the last minute, or the positive, that we played very well in general, that we absolutely controlled the first half, and dominated the second.
“It’s a long and difficult competition. I don’t know what people expected, that we were going to win it by 20 points? We know it is going to be difficult.”
Real Madrid boss Zinedine Zidane said: “It’s a point, we’re alive and we’re going to keep fighting.
“There’s still a long way to go in La Liga and a lot of points at stake, we’re going to fight until the end.
“Things can change quickly. We’re doing the right things, although we know we can improve and that’s what we’re going to do.
“We wanted to play better in the second half today because the first half wasn’t good. The attitude was very important to change things.”