Had the former Barcelona ace, who has yet to impress since returning home from AC Milan in January, converted the penalty in the fourth minute of added time Flamengo would have avoided the Brazilian champions.
"I kicked it badly and the ball rose. That's how it is. At the right time, I'll get goals," Ronaldinho told reporters.
Carioca title holders Botafogo are the only one of Rio's four big teams to have failed to reach the semi-finals in the second stage of the state championship.
Modest Olaria have taken their place and will face Vasco da Gama in the other semi-final.
Flamengo, who won the first stage of the championship, will be crowned champions if they also win the second phase. Otherwise they will have to face the winners in a grand final.
The state championships precede the Brazilian first division championship that starts next month.
The Paulista (Sao Paulo) and Gaucho (Rio Grande do Sul) championships have reached the quarter-final stage.
Former Brazil midfielder Falcao made his debut as coach of South American champions Internacional with a 1-0 win over Santa Cruz, young Brazil striker Leandro Damiao scoring the only goal, on Saturday.
