Brazil now need a draw in their final game against Serbia to ensure their passage through to the knockout stages. But, after an exemplary use of the video assistant referee (VAR) system, the referee decided that the contact did not merit Neymar's tumble and changed his mind.
The scrutiny will be on Neymar, but Brazil have a team packed full of talent that can hurt Costa Rica.
Brazil were frustrated by Los Ticos until second-half stoppage time, when Philippe Coutinho found the breakthrough and, with the pressure off, a free-wheeling Neymar added a second before the final whistle.
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Japan beat 10-man Colombia 2-1 in group H yesterday to become the first Asian side to beat a South American one at the World Cup. Senegal emerged victorious by beating Poland 2-1 in the Group H encounter.
Celso Borges spurned arguably the best chance of the first period for Costa Rica when he ran on to Gamboa's cut back but shot wide from eight metres out.
In the end, Brazil found the net with Philippe Coutinho prodding home a late victor through the legs of Keylor Navas.
As was the case against Switzerland on Sunday, Neymar was on the receiving end of some physical treatment from Costa Rica's defenders but he didn't feel he was adequately protected.
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After Brazil's Neymar took a spectacularly languid fall in the penalty area, social media users wasted no time in pointing out how unconvincing it was.
Brazil had many chances throughout the game, with Costa Rica avoiding disaster through a strong defensive performance and the virtuosity we have come to expect from Navas.
- Brazil have won 10 of their 11 meetings with Costa Rica in all competitions, losing the other in a friendly in 1960.
The defeat ended Costa Rica's World Cup campaign as they bowed out after two straight defeats. Rushing the field to celebrate the first goal, he got tripped up and tumbled to the grass.
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Granit Xhaka and Xherdan Shaqiri celebrated their goals by making a nationalist symbol of their ethnic Albanian heritage. Follow live updates from Group E as Serbia take on Switzerland .
Similarly, Neymar became used to Brazilian referees giving him a free kick for every minor contact and fall.