Just after the spirited opening ceremony in Sao Paulo, many of the roughly 60,000 soccer fans in the Corinthians arena chanted profanities at Rousseff, who was seated in a skybox at the stadium.
Some also directed obscenities at FIFA, soccer's governing body.
More jeers came from fans watching the game at outdoor venues when an image of the president, wearing patriotic green, appeared on giant screens in cities including Sao Paulo, Rio de Janeiro and Brasilia, the capital.
Despite raucous support for the national team, many Brazilians are angered by their government's extravagance - more than $11 billion in World Cup spending - at a time when the country's economy is sagging and public services are in dire need of investment.
Rousseff, a leftist who will make a bid for re-election in October but has seen her popularity slide over the past year, chose not to speak at the ceremony. Earlier on Thursday she hosted a lunch for eight other heads of state who were expected to be in attendance at the international sports event.
Last June, at the opener of the Confederations Cup, a warmup tournament to this year's main event, she was jeered loudly when she declared the tournament open. Massive street demonstrations proceeded across Brazil for the remainder of the competition.
Just after halftime, Brazil and Croatia were tied with one goal each - an own goal early in the game by Brazilian defender Marcelo and an equalizer by star forward Neymar.
(Reporting by Paulo Prada; editing by Gunna Dickson)