Valencia's stirring victory at their Mestalla stadium briefly lifted them above Barcelona to the top of the standings before Lionel Messi and Neymar struck in a 2-0 success at Rayo Vallecano, who had two players sent off, to restore Barca's two-point advantage.
The Catalan club are the first La Liga team to avoid conceding a goal in their opening seven matches of the season.
Valencia last won the Spanish league title in 2004 but have started their latest campaign in impressive form and made a thrilling start at the Mestalla to race into a 3-0 lead by the 13th minute.
Atletico centre back Miranda put the ball into his own net in the sixth minute, Andre Gomes finished superbly after a fine run a minute later and Nicolas Otamendi nodded in at a corner to leave the champions reeling.
Mario Mandzukic pulled a goal back in the 29th when he followed up a Tiago effort to head home before Atletico squandered a chance for a second on the stroke of halftime.
Valencia goalkeeper Diego Alves, a penalty specialist, saved Guilherme Siqueira's weak spot kick, the 13th the Brazilian has stopped out of 31 faced in La Liga.
Showing little sign of fatigue after their 1-0 success against Juventus at the Calderon, Atletico pushed hard to get back into the match but the home side comfortably held on and Alves was barely tested in the second period.
Atletico's Italy winger Alessio Cerci had a miserable afternoon when he came off the bench in the second half, picked up two yellow cards and was sent off.
The second card was awarded in added time when he sprung the offside trap and put the ball in the net but the referee ruled he had used his arm to control it.
Valencia, who failed to qualify for European competition last season, have 17 points from seven matches, with Barca, who are unbeaten and yet to concede a goal, on 19.
Atletico have 14 points in third and can be overtaken by Real Madrid, Sevilla and Celta Vigo if they all win on Sunday.
ITENSITY, AGGRESSION
"The first goal was a defensive error by a team that normally doesn't commit them," Valencia coach Nuno told a news conference.
"We have beaten a great football team, the current champion, but they are only three points," added the Portuguese, a former Deportivo La Coruna and Porto keeper who took over at the end of last season.
"We showed incredible intensity and aggression and if I was a spectator I would go away happy at having seen a good game."
Atletico coach Diego Simeone acknowledged his players had made uncharacteristic errors but said he was pleased with the work they had put in to try to get back into the game.
"There are times when you lose with dignity having given everything on the pitch," he told a news conference.
"They (Valencia) are not playing in Europe this season and with the squad they have they will have to play very badly not to finish third or fourth," added the Argentine.
Barca took time to get going at Rayo's Vallecas stadium in the Madrid suburbs before Messi scored a typically brilliant effort in the 35th minute.
The four-times World Player of the Year ran on to a lofted Gerard Pique pass, shrugged off a defender and sent a wonderful dinked effort over Rayo keeper Tono into the net from a tight angle on the left of the area.
Neymar added a second a minute later when he picked up a Munir El Haddadi layoff and smashed a low shot into the bottom corner.
Rayo defender Jorge Garcia was shown a second yellow card and sent off on the hour and although Barca then took their foot off the gas they could have added to their tally several times, with Messi especially wasteful.
Rayo substitute Javier Aquino picked up his second yellow card in the first minute of added time.
The match was also noteworthy for Barca's Chile keeper Claudio Bravo setting a record for minutes unbeaten at the start of a La Liga season.
During the first half Bravo surpassed the previous best of 560 minutes set by former Barca and Sociedad keeper Pedro Maria Artola in 1977-78.
(Writing by Iain Rogers, editing by Pritha Sarkar)
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