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The hosts went ahead in the second minute of this FIFA World Cup qualifier in Santiago when a looping header from Eduardo Vargas went past Ederson in goal, although it was an effort that should arguably have been saved.
While Chile had chances to extend its lead and had claims for a penalty in the first half, Brazil equalised in stoppage-time through a close-range header from Igor Jesus.
The Selecao controlled much of the second half as it went in search of a winner, and was able to find it a minute from time.
Botafogo winger Luiz Henrique cut in from the right and bent a shot past the goalkeeper to earn his country three points.
It is a victory that moves Brazil up a place to fourth in the CONMEBOL qualifying table for the FIFA World Cup, while Chile remains second-bottom, seven points behind an automatic qualification spot.
Prior to this victory, Brazil had been on a run of four defeats in five matches in FIFA World Cup qualifying.
This result leaves it three points ahead of eighth-placed Paraguay, which occupies the final elimination slot and beat Brazil 1-0 in the previous matchday.
Although Brazil found a way to win, this was the sixth qualifier in eight that it registered three shots on target or fewer.
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