A Neymar corner was headed straight at Navas by Silva, and then Neymar won the ball back inside the Costa Rica half and raced to the edge of the area but whipped the shot wide.
Neymar was taken nearly completely out of the match by the Swiss defense, racking up 11 fouls against him.
After frustrating the Brazilians for 90 minutes, the Costa Ricans finally conceded twice in stoppage time and slumped to a second loss that ended their chances of advancing to the knockout stage.
"Things were never easy in my life, so why would they be now?"
In Brazil's opening match against Switzerland, a 1-1 draw, Neymar was fouled 10 times.
Neymar added the second with practically the last kick of the game, racing on to Jesus's square ball following a quick counter-attack as Costa Rica were forced to push for the equaliser.
Neymar missed the end of Paris Saint-Germain's season after undergoing surgery on a fractured metatarsal in March.
Tite, meanwhile, was left limping, after the 57-year-old reacted to Coutinho´s strike by bursting onto the pitch and tripping over his own feet. "Brazil doesn't need any help".
The PSG forward, 26, scored late for Brazil to wrap up all three points for the South Americans.
The iconic striker fired Brazil to 2002 World Cup glory and it's now been revealed what he's been doing for the world's most expensive footballer in Russian Federation.
Do you think Costa Rica could upset Brazil in this fixture?
The final stretch of the game proved to be a frantic affair, with Tite's side chasing the game, but the five-time World Cup champions managed to find a crucial late goal when Phillipe Coutinho stabbed the ball home in the 91st minute of the game.
Tite said that Neymar, who endured a lengthy spell on the sidelines with a metatarsal injury before the World Cup, is still regaining form and full fitness as Brazil's Group E campaign unfolds.
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