The two Spanish heavyweights dropped points in their previous games but returned to winning ways with dominant home performances engineered by their two outstanding players.
Valencia suffered their first defeat of the season when they were beaten 1-0 at nine-man Sevilla and Athletic Bilbao's new coach Marcelo Bielsa is still without a win after the Basque club surrendered the lead in a 1-1 draw at home to Villarreal.
Champions Barca, bidding for a fourth straight title, have 11 points from five games, level with third-placed Sevilla and one ahead of Real Madrid and Valencia.
Promoted Real Betis, the surprise early leaders, have 12 points from four games and visit Getafe on Monday.
Atletico had the first clear chance at a rainy Nou Camp when Jose Antonio Reyes squared for Tiago and the Portuguese midfielder curled a shot from the edge of the penalty area that struck the crossbar.
That was as good as it got for Gregorio Manzano's side as Barca, who drew 2-2 at Valencia on Wednesday, were ahead in the ninth minute.
A superb pass from playmaker Xavi sent David Villa clear and he turned inside his marker before rifling a low shot past keeper Thibaut Courtois.
Barca doubled their lead six minutes later when World Player of the Year Messi and Pedro combined and the ball deflected in for an own goal off defender Joao Miranda.
Messi made it 3-0 in the 26th minute when he flummoxed the Atletico defence with an outrageous piece of skill before curling a precise shot inside the post.
His second came after a trademark run across the defence and shot back across the keeper and he completed the hat-trick in added time when he ran on to a Villa chip and shot through the legs of Courtois from a tight angle.
At the Bernabeu earlier, Real got the morale-boosting win they were looking for after a shock 1-0 defeat at Levante and a 0-0 draw against Racing Santander in their previous two games.
The home support were given an early fright as Vallecano, whose annual budget is a fraction of their illustrious city neighbours, scored a goal timed at 12 seconds when Michu followed up a blocked Raul Tamudo effort.
The visitors had a couple of chances to extend their lead, prompting frustrated whistling from the home fans before Ronaldo equalised in the 39th minute and Gonzalo Higuain put Real ahead in first-half stoppage-time.
Ronaldo, who scored three against Real Zaragoza last month, made it 3-1 from the penalty spot in the 51st after Kaka was felled but Michu scored a second goal four minutes later.
Home forward Angel di Maria then picked up a second yellow card and was sent off after 56 minutes.
Real restored their two-goal lead when teenage defender Raphael Varane diverted a corner into the roof of the net.
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