La Liga leaders FC Barcelona lost 1-0 at Real Sociedad on Sunday after Lewandowski's goal was controversially disallowed, with coach Hansi Flick calling the decision "a big mistake".
Julian Alvarez earlier helped Atlético Madrid to a 1-0 victory in Mallorca, allowing the Rojiblancos to move up to third.
Sheraldo Becker's 33rd-minute goal condemned Barcelona to their second league defeat of the season, leaving the Catalan giants six points clear of second-placed Real Madrid after playing extra time.
Lewandowski's disallowed goal early in the match led to a furious debate over whether the Polish striker was offside or not.
"It was a bad decision, it's clear, but we have to accept it," Flick told the club's broadcast platform, Barca One. "The referee, it wasn't his fault, we're human, we make mistakes and today was a big mistake."
Barcelona were without young star Lamine Yamal, who suffered a sprained ankle during the Champions League win against Red Star Belgrade in midweek, and almost lost their spark.
The Catalans failed to score in a game for the first time this season in all competitions, with eighth-placed Real Sociedad holding on, while Barcelona failed to register a shot on target.
"The responsibility for this loss is on us, we are responsible, we can play much better," admitted Flick.
"It's a difficult place to go, where Real pushes a lot... we have to learn from our mistakes and that's it," Barcelona midfielder Pedri told Movistar. "Normally we score goals, but today we were not precise, I think it will be an isolated case and in the next games, we will be more precise.
"I think the team is working well and (not scoring) is not something that worries me."
The manager Dani Olmo started on the bench, while the defender Pau Cubarsi played in a mask after suffering a cut to the face that needs points in Serbia.
The Catalans have struggled in San Sebastian in the past and had another unpleasant evening in the Basque Country.
Lewandowski thought he had given Barcelona the lead after 13 minutes when he reacted well after a blocked shot to score, but the goal was disallowed after a VAR review.
Referee Guillermo Cuadra Fernandez was informed that Lewandowski was offside, although he did not appear to be in contact with Real Sociedad defender Nayef Aguerd. The semi-automated offside technology used in La Liga indicated that the front of Lewandowski's boot was wrong, but Spanish media furiously debated whether the technology had misinterpreted Aguerd's heel as part of the veteran's boot striker.
Real dominates
Despite the Barça goal, the home team took control and tested visiting goalkeeper Inaki Pena on several occasions.
Takefusa Kubo's low shot stung Pena's fingers after a good dribble inside from the Japan international's right.
Becker gave Real Sociedade the lead with a low shot after Luka Sucic headed the ball towards him.
Flick brought on Dani Olmo for an ineffective Frenkie de Jong in the first half, but Barcelona came second.
Becker missed his shot after Jules Kounde did enough to deny the Real Sociedad winger and Ander Barrenetxea also fired wide from a tight angle after breaking into the box. Despite scoring 40 goals in the first 12 league games, Barcelona failed to find the back of the net or create any danger in the latter stages.
"We wanted to win at home and there was no better team to do it," said Real Sociedad midfielder Brais Mendez.
"They are the best team in Europe and the fans deserved a night like this."
Diego Simeone's Atlético secured a fourth straight win in all competitions in a close encounter at Mallorca's Son Moix Stadium.
Alvarez scored his fourth league goal since joining Atlético from Manchester City in the summer in the 61st minute after being served unselfishly by Diego Simeone's son Giuliano Simeone.
"We knew it would be a difficult game, we improved in the second half, the goal came and we got three important points," said Argentina's Alvarez.
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