In other third-round, second-leg ties, defending champions Boca Juniors won 2-1 at Cruzeiro to complete a 4-2 aggregate victory and Adriano scored to set Sao Paulo on the way to a 2-0 win over Nacional which put them through.
America, beaten 4-2 in the first leg and under interim coach Juan Antonio Luna, contrived to win the return leg 3-0 at the Maracana to leave Santana wishing he had not agreed to extend his stay at Flamengo for an extra game.
Santana, who is due to arrive in Johannesburg early tomorrow, had been due to sign off last Sunday when Flamengo beat Botafogo 3-1 to win the Carioca championship.
Instead, he agreed to see the team through what appeared to be a formality before handing over the reins to Caio Junior.
“I told them that the best tribute you can pay me is to qualify,” said Santana. “It’s difficult to explain a defeat like this. We lost to ourselves.”
On Sunday, Flamengo fans were celebrating the Campeonato Carioca title and praising Santana for his great work, but after yesterday’s match police had to intervene as a portion of the 50 000 irate football followers stoned their team’s bus.
At the final whistle, a disdained-looking Santana could hardly believe what had happened - as his players drooped off the pitch, some in tears.
Trying to explain the inexplicable, he said, “To explain is difficult. I told the players in Mexico that it wasn’t finished. Yesterday, I was worried and we conceded two unbelievable goals. America had five chances and we were unable to compete.
“The team tried, but we were incapable, it’s not the end of the world, but we’re out of a competition which was almost guaranteed.”
When asked if this was his worst defeat, Santana added: “There have been others which have hurt a lot, one or two where we lost the title in the last minute. Let’s not crucify the athletes, they never gave up trying.
“Sometimes we just have to remain quiet. We know what happened. I know there were many people who paid homage to me, I wanted a victory, but it wasn’t to be.”
Flamengo’s problems began when Paraguay striker Salvador Cabanas lobbed the ball over Bruno in the 20th minute to put the Mexicans ahead.
Enrique Esqueda levelled the aggregate scores six minutes before halftime, although Flamengo were still leading on away goals.
Cabanas struck the final blow when he scored with a deflected free kick in the 78th minute.
Flamengo’s fellow Brazilians Cruzeiro also went out at home after Boca struck twice in 10 minutes before halftime.
Rodrigo Palacio cut inside his marker and fired a 20-metre shot into the top corner and Martin Palermo added the second with a header. Wagner pulled one back for Cruzeiro in the 57th minute.
Sao Paulo, who drew 0-0 at Nacional last week, provided Brazil’s only success of the evening at the Morumbi.
Adriano, on loan from Inter Milan, scored from close range in the 38th minute after two Nacional defenders failed to cut out Eder Luis’s pass.
The Uruguayans had Pablo Caballero sent off for a second bookable offence at the start of the second half and Dagoberto added Sao Paulo’s second in the 89th minute.