Earlier, Barca also weren't at their best but Luis Suarez's double ended a five-game goal drought for the Uruguayan and Paulinho's late strike helped see off a determined Leganes 3-0.
Angel Correa missed the best chance of the game after just three minutes as both Atletico and Real were left to rue a familiar lack of cutting edge in front of goal this season.
After a bright start from Atletico, Real's first chance came on the counter-attack but Juanfran outpaced Cristiano Ronaldo when the Portuguese was put clean through by Luka Modric much to the home crowd's delight.
The visitors slowly started to take control of possession as the first period wore on, but lacked a creative spark.
Jan Oblak turned Toni Kroos's effort behind at the near post after a neat one-two with Ronaldo, before Sergio Ramos was left bloodied and eventually replaced at half-time as he was caught by Lucas Hernandez as he stooped to head into the side-netting.
Ronaldo's profligacy has been blamed for Real's slump in form this season and the Portuguese was once again wayward when handed the chance to win the game 15 minutes from time.
Modric picked out the World Player of the Year unmarked inside the Atletico box, but Ronaldo's tame effort dribbled wide.
Both sides had chances to win it in a frantic finale as Raphael Varane headed Kevin Gameiro's lobbed effort off the line.
At the other end, Ronaldo took just too long to wind up his effort as Hernandez galloped back into position to make a brave block and ensure Atletico a share of the spoils.
Barca boss Ernesto Valverde admitted a 3-0 win flattered his side across Madrid at Butarque as goalkeeper Marc-Andre ter Stegen again shone.
"The important thing was to win," Suarez told BeIN Sports Spain. "We always try to play our best in every game but sometimes it is not possible."
Leganes' good work in the opening half hour was undone by a goalkeeping error when Ivan Cuellar limply palmed Paco Alcacer's driven cross into the path of the grateful Suarez to smash home his first goal for a month.
"I wasn't anxious. The important thing was to feel good again and help the team," added Suarez.
Barca's joy was tempered moments later when Gerard Pique was booked for bringing down Nordin Amrabat meaning he will be suspended for next weekend's top of the table clash at Valencia.
The busy Ambrabat was the creator for Leganes' best chance before the break when he released Alexander Szymanowski inside the area, but the Argentine's curling effort was turned to safety by the in-form Ter Stegen.
The German goalkeeper was called into action again early in the second period when Leganes substitute Claudio Beauvue was too quick for the Barca defence only to fire straight at Ter Stegen.
In contrast, just as in the first half, Barca were ruthlessly efficient in front of goal to double their lead on the hour mark.
Lionel Messi's dinked pass released Alcacer and after Cuellar parried his first effort, Suarez drilled home the rebound for his second of the afternoon.
Barca rode their luck to hold out for a 12th clean sheet in their last 17 games as Ter Stegen saved one-on-one from Amrabat and Beauvue blasted well over when unmarked 10 yards out.
"Perhaps 0-3 is a bit excessive. They played well enough for the gap between the teams to not be so great," said Barca boss Valverde.
However, Barca rubbed salt into Leganes' wounds when Paulinho rolled into an empty net when a loose ball broke off Messi in stoppage time.
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