Neymar and Luis Suarez were on target as Lionel Messi orchestrated a dazzling first-half display at Camp Nou.
Rumours of a rift between head coach Luis Enrique and Messi made for numerous uncomfortable headlines in Catalonia this week and the Argentina superstar was in the unfamiliar position of giving away a 57th-minute penalty.
Mario Mandzukic converted to give Atletico a lifeline and Barca endured some nervous moments before Messi sealed the points three minutes from time.
Luis Enrique's team are a point behind leaders Real Madrid having played a game more and Atletico lie three points further back in third.
Seville are now only two points behind the champions with a game in hand after they won 2-0 at Almeria in the early kick-off.
Vicente Iborra and Coke scored within five second-half minutes of one another to prevent the resurgent hosts from extending their unbeaten run in all competitions to five matches.
Real Sociedad served to heighten the recent scrutiny on Luis Enrique with a memorable 1-0 win over Barca in San Sebastian last weekend and they followed up that result with a 1-1 draw at Granada.
The game proved to be a tale of two penalties, with Carlos Vela netting in the 36th minute for Sociedad after Sergio Canales was fouled.
Fran Rico kept his cool 11 minutes from time to ensure a share of the spoils for Granada.
A point could not stop Joaquin Caparros' side slipping to the bottom of La Liga as 19th-place Elche sealed a shock 2-1 victory at Athletic Bilbao, winless in five league games.
