Football's governing body Fifa said Lopez could not perform at Thursday's event as planned earlier because of unspecified "production issues".
The singer's representatives did not explain the reason why Lopez would not be joining the act, confirming only the announcement in an emailed response, saying: "Regretfully Jennifer Lopez will not be attending this year's World Cup opening ceremonies."
Fifa said Cuban-American rapper Pitbull and Brazilian singer Claudia Leitte would sing the official tune We Are One before Brazil played Croatia at Thursday's opening game in Sao Paulo.
The song has let down many Brazilians who complain that it sounds too generic for the nation's Bossa Nova-crazed audiences and that it features foreign musicians singing mostly in English and Spanish.
Leitte sings only a few seconds at the end of the song in her native Portuguese.