The 22-year-old was stretched off in the dying minutes of the Selecao's game in Fortaleza and was seen to be in distress as he left the field, following a challenge from Juan Camilo Zuniga.
Team doctor Rodgigo Lasmar later confirmed that Neymar had fractured a vertebra in his back and admitted that Brazil's top scorer will need a few weeks to recover.
Lasmar told SportTV: "Unfortunately, he's not going to be able to play.
"It's not serious in the sense that it doesn't need surgery, but he'll need to immobilise it to recover."
Brazil will also be without captain Thiago Silva when they face Germany in Tuesday's semi-final.