Two first-half efforts left the Catalans leading before Mario Mandzukic's penalty set up a tense finale, but the four-time Ballon d'Or winner sealed the win very late on
Head coach Luis Enrique was criticised by many for his team selection in last weekend's dispiriting 1-0 loss at Real Sociedad and a 5-0 midweek thrashing of Elche in the Copa del Rey did not prevent him from entering Sunday's pivotal Camp Nou encounter under heavy scrutiny.
A rumoured rift between Luis Enrique and Lionel Messi dominated the pre-match build-up, but Barcelona's star man produced a majestic and tenacious display, laying on goals for attacking colleagues Neymar and Luis Suarez to ensure the hosts led 2-0 with 10 minutes to until half-time.
Messi blotted his copybook by conceding a soft 57th-minute penalty that Mario Mandzukic converted to hand Atletico a lifeline, although Diego Simeone's men could not follow Wednesday night's stirring 2-0 cup win over city rivals Real Madrid with another memorable success on the ground where they famously secured the Liga crown on the final day of last season.
It was Messi who fittingly had the final word, ending a run of seven goalless matches against Atletico three minutes from time and closing Barca to within two points of leaders Real having played a game more
Atletico are three points further back in third after a match where their enterprising start quickly unravelled into a torrid opening half.
Messi skewed a ninth-minute shot wide but created the opening goal from the inside-right position.
Suarez failed to control his team-mate's low cross with his thigh but Juanfran's missed clearance left Neymar with a far-post finish.
It was almost double misery for Atletico in the 13th minute as goalkeeper Miguel Moya fumbled a Neymar strike and recovered sharply to thwart Suarez.
The visitors responded in robust fashion as a shuddering tackle from Jose Gimenez left Neymar with a bloodied right ankle and left-back Jesus Gamez - seemingly targeted by Barca on his second league start for Atletico - was booked for clattering through Messi.
On his return to the field, Neymar passed up a glorious 23rd-minute chance to double his tally with a back-post header after Messi sent Suarez scampering away down the right.
Moya stood firm to deny Messi when some dazzling footwork left Gamez in his wake and the mercurial Argentine was to the fore when Barca doubled their lead, albeit with a slice of fortune.
Referee Alberto Undiano Mallenco did not penalise Messi for an apparent handball before a driving run left the Atletico defence is disarray and allowed Suarez to slam home his second Liga goal.
Any ill-feeling from Simeone's men towards the official was partially undone 11 minutes into the second half when, in an unlikely role reversal, Messi clipped Gamez's ankle in the area and Mandzukic blasted the resulting penalty - and his team's first shot on target - high into the centre of the goal.
Atletico turned up the heat during the closing stages, when tempers threatened to boil over on both sides, but they were unable to fully wrestle control from Barcelona.
Following a particularly fractious period of play, Messi converted a slotted pass from the excellent Ivan Rakitic at the second attempt to ensure Barca overcame an opponent they failed to beat over six games last season.