The 29-year-old picked up the injury in training and will return to club side Paris Saint Germain as a result.
Neymar starred in Brazil's previous game against Colombia, providing the crucial assist for Lucas Paqueta to score the only of the game as Tite's men secured passage to the 2022 FIFA World Cup in Qatar.
"Due to a thigh injury Neymar will not play against Argentina, this Tuesday (November 16th), for the WC Qualification," a statement from the Brazilian Football Confederation (CBF) read.
"Neymar didnt travel to Argentina with the rest of the Brazilian squad and will return to France this Wednesday."
A statement from CBF to GE.com added: "After the activities held on Palmeiras' Football Academy on this Monday morning, Neymar complained about feeling pain in his left thigh.
"Neymar Jr. revealed insecurities about the situation and as a result of not having enough time to make complementary medical exams, Brazilian technical staff decided to preserve the player, who will not travel with the Brazilian Group to San Juan, where the game against Argentina will take place this Tuesday."
Lionel Messi is however fit to feature from the start for Argentina after playing a cameo role in their win over Uruguay last time out.
Brazil are top of the South American qualifying group with 34 points, six points clear of second placed Argentina.
