Friburguense striker Victor Hugo's 47th minute effort in Sunday's match at the Maracana was ruled out by the linesman as television replays showed three defenders between the forward and the goal at the time he received the ball.
Globo television's website Globoesporte described it as "an unbelievable offside" and a "grotesque mistake".
Five minutes later, left back Juan scored for Flamengo to give his side a 1-0 win with Friburguense claiming that their goalkeeper had been fouled in the build-up.
The first full weekend of the Brazilian season had got off to an even more controversial start on Saturday when Botafogo were initially awarded a goal against Boavista when replays showed the ball had gone in through a hole in the side-netting.
Play was interrupted for 10 minutes as the referee twice confirmed the goal after consultations with his linesman, then changed his mind after more deliberations with the fourth official.
Botafogo later suggested that officials had used television evidence to make their decision.
Brazilian champions Sao Paulo won their first match of the year as they beat Portuguesa 2-0 with both goals coming from new signing Washington.
The player known as Braveheart opened his account from a corner in the first minute and got in front of the Portuguesa defence to head the second in the 78th minute of the Paulista championship.
Ronaldo's new club Corinthians notched a 1-0 win at Bragantino in the same tournament as they wait for the former Real Madrid, Barcelona, PSV Eindhoven and AC Milan player to make his debut.
Ronaldo, who suffered a serious knee injury last February, is expected to make his debut next month.
The Paulista and Carioca championships are the largest of the regional tournaments which serve as a prelude to the Brazilian championship.
