The 42-year-old from Tokyo will be assisted by compatriots Toru Sagara and Toshiyuki Nagi for the game at the Itaquerao stadium in Sao Paulo, while Iran's Alireza Faghani will be the fourth official.
Nishimura refereed four games at the 2010 World Cup in South Africa, including Brazil's 2-1 quarter-final defeat to the Netherlands, where he sent off the Selecao's Felipe Melo in the 73rd minute of the encounter for a stamp on Oranje star Arjen Robben.
Fifa have also appointed Italian referee Nicola Rizzoli to oversee the highly-anticipated Group B clash between Spain and Netherlands in Salvador on Friday - a rematch of the tumultuous final that Spain won 1-0 four years ago.
The match will be a first World Cup game for Rizzoli, who took charge of the 2013 Champions League final.
Of the the 25 referees involved in the tournament in Brazil, Nishimura is one of five that took part in the World Cup in 2010, where he was fourth official for the final.
The other four are Uzbekistan's Ravshan Irmatov, Joel Aguilar of El Salvador, Peter O'Leary of New Zealand and England's Howard Webb, who officiated the final.