Atletico were chasing a first La Liga derby double in 63 years, with the 1950-51 season also being a title-winning campaign, but they were ultimately denied by Carlo Ancelotti's side at Vicente Calderon.
After Karim Benzema had given Real the lead, Atletico went into the break 2-1 ahead after Koke's low finish and Gabi's long-range effort.
In what was an ill-tempered encounter, Diego Costa saw numerous penalty claims ignored and when he was controversially shown a yellow card for simulation, Atletico coach German Burgos had to be restrained as he confronted referee Carlos Delgado.
Real stole a late point thanks to Cristiano Ronaldo's 23rd La Liga strike of the season and in doing so kept the club's unbeaten run going, extending their streak to 28 straight games in all competitions without losing.
Barcelona's win over Almeria was a comfortable one, but they should have scored more than four.
Alexis Sanchez gave them an early lead before Lionel Messi netted his 229th La Liga goal, overtaking Real legend Raul as the division's all-time third highest scorer with an excellent free-kick.
Angel Trujillo got Almeria back into the contest as he headed in a corner and although the hosts wasted countless chances in the second half, they did eventually wrap up the win late on.
Carles Puyol tapped in from close range after Messi had hit the crossbar with a header and Xavi completed the scoring with a superb finish from just outside the penalty area.
In the race for UEFA Champions League and Europa League places, Sevilla moved back up to seventh thanks to a 1-0 win over Real Sociedad at the Ramon Sanchez Pizjuan.
Unai Emery's home side had the better of the encounter and they eventually secured all three points 13 minutes from the end as Kevin Gameiro prodded home from close range, leaving Sevilla five points behind their sixth-placed visitors.
Valencia slipped three points behind the Andalucians as they suffered a 1-0 defeat at Rayo Vallecano.
Joaquin Larrivey scored the only goal of the game on the hour, before Antonio Barragan was shown a second yellow card for Valencia in the 76th minute.
Although Rayo remain in the bottom three, they are now just three points behind Almeria in 17th.
Sunday's early kick-off saw 10-man Villarreal drop two points at home to basement club Real Betis, with Ruben Castro cancelling out Bruno Soriano's opener shortly after Ikechukwu Uche had been sent off for the hosts.
