Internacional lost 3-1 away to Argentina's Banfield and Sao Paulo drew 0-0 with Peruvian champions Universitario in Lima. Both Brazilian teams had players sent off.
A crowd of 72,000 gathered at the Maracana to watch the clash between Brazil's two most popular teams after contrasting results in the group phase.
A first half in pouring rain gave way to a better second and Brazil's Adriano converted a 64th minute penalty, his first goal for a month, after left back Juan was brought down by Moacir.
It was Flamengo's first match since sacking coach Andrade, who had steered them to the Brazilian title last year, after a poor group performance.
"In our circumstances, I think the victory was excellent. Congratulations to the players who honoured this shirt in a marvellous way," said caretaker coach Rogerio Lourenco, Andrade's former assistant.
In Buenos Aires, Colombian forward James Rodriguez scored his fifth goal of the competition to put Banfield ahead less than two minutes into the second half. He ghosted in unmarked on the left to shoot from a tight angle past Inter's Argentine keeper Roberto Abbondanzieri.
Tempers flared for a few minutes when Inter's Uruguayan coach Jorge Fossati was hit on the head by an object thrown from the crowd.
"We beat a great rival. Luckily we got a good difference (in the score) but it's not decisive," Erviti told Fox Sports.
