Uruguayan striker Diego Forlan scored his 18th goal of the season for Atletico late in the first half, but Dutchman Klaas-Jan Huntelaar equalized early after the break.
Barcelona, which had lost its previous games, won on goals by Sergi Busquets and Lionel Messi.
The only bad news for Barcelona was that defender Carles Puyol could miss the next three weeks out because of twisted ankle ligaments suffered in the 90th minute.
One of the reasons given for Barca's defensive problems has been the absence of French left back Eric Abidal, which forced Puyol to move from the middle of the backline to the left side.
With Abidal still out, Brazilian Sylvinho should line up on the left against Lyon in the Champions League on Wednesday.
Struggling Valencia's problems continued as it blew an early lead and fell to lowly Numancia, 2-1.
Beset with financial problems, Valencia got more bad news when its star, Spain striker David Villa, hurt his knee in training.