Selecao eventually sealed the win in second-half stoppage time as Roberto Firmino out-muscled his marker before lobbing the ball into the back of the net.
The defeat was Croatia's second in their last three friendly games (won one) ahead of the FIFA World Cup.
The Brazilian injured the same foot playing for Paris Saint-Germain and underwent surgery in Brazil in early March.
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Brazil will undoubtedly be careful with the 26-year-old, who is arguably their most important player.
Brazil striker Neymar made a spectacular return on Sunday after a three-month absence with a foot injury and celebrated a superb individual goal with his surgeon.
The Barcelona midfielder looked likely to depart Anfield last summer when it was obvious that Barcelona wanted to sign him and that he wanted to go.
He formed part of a potent three-man forward line that also featured Chelsea's Willian and Manchester City's Gabriel Jesus, who was named captain for the day, the 15th player to wear the armband under the reign of manager Tite.
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Russian Federation 2018 will be Neymar's second World Cup finals.
Croatia's hard pressing had frustrated Brazil in the first 45 minutes and they needed keeper Alisson to get down well to keep out a drive from Andrej Kramaric after Miranda gave the ball away.
"Neymar? He'll start on the bench because he's still recovering, and will come on at half-time because we're preparing as a team", Tite told reporters at a press conference on Saturday.
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