Brazil had a closed practice session Wednesday, two days before its game against Costa Rica in St. Petersburg, but the federation posted photos and a video of Neymar in action in training with the rest of the squad.
The Paris St Germain forward spent much of the match rolling on the floor as the Swiss, who committed 19 fouls, 10 of which were on Neymar, tested his injured foot.
The federation said he left the session only as a precaution because he had been in pain since the team's 1-1 draw against Switzerland on Sunday, when he was consistently fouled.
"Neymar is one of the best players in the world and it's a great plus to have him in the team, " said Philippe Coutinho, who has gained a bigger role as Neymar struggles with his fitness.
The world's most expensive player then set alarm bells ringing when he hobbled out of training on Tuesday in full view of the cameras.
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But as numerous World Cup favourites have found so far in Russian Federation, friendly performances mean little when the competition kicks off for real and Brazil were found wanting against an aggressive and well-organised Swiss side.
The Selecao need their talisman at his best after drawing 1-1 with Switzerland in their 2018 FIFA World Cup opener, and the Mirror's Alex Richards reported on his withdrawal, which comes after Neymar only recently recovered from a broken foot.
And Neymar's importance in this new-look team - he is one of only six survivors from four years ago - is clear from the comments of his teammates in Sochi.
Switzerland coach Vladimir Petkovic highlighted the personality his side had shown in coming back from behind to earn a draw against one of the favourites for the title.
Brazil meet Switzerland in the newly-built 45,000 Rostov Arena in Sunday's evening game but before that Germany play Mexico in a mouth-watering tie in Moscow's Luzhniki Stadium. The last time they lost their first game in the tournament was in 1934 against Spain (3-1).
However, it was Behrami's performance that saw Switzerland keep Brazil's most risky player silent and deservedly win one point from the game.