Uruguayan giants Nacional clinched pole position in Group One of the Copa Libertadores, despite losing 1-0 to Ecuador's Barcelona on Wednesday.
The only goal came in the 36th minute, as Luis Caicedo set up Gonzalo Castillejos for a close range finish to win it for the home side.
However, Boca Juniors were unable to record the win they needed to finish top of the group, falling 3-2 in their visit to Mexico's Toluca.
Boca, the Libertadores runners-up, needed to win and wait for Nacional to lose in their visit to Guayaquil, but Carlos Bianchi's squad wasted their chances.
Home forward Edgar Benitez broke the deadlock early on - but midfielder Leandro Somoza headed home Juan Roman Riquelme's corner in the closing stages of the first half to level the clash.
Flavio Santos fired the hosts once more but youngster Guillermo Fernandez volleyed in for the Argentinians - only for Santos to head in the winner for Toluca from a corner.
Nacional ended with 10 points from six games, one more than Boca, two more than Toluca and four more than Barcelona.
Elsewhere, Copa Sudamericana reigning champions Sao Paulo grabbed second place in Group Three with a 2-0 win over group winners Atletico Mineiro 1-0.
Second half goals from Rogerio Ceni (penalty) and Ademilson saw them pip Argentina's Arsenal for second place on goal difference.
Arsenal defeated Bolivia's The Strongest 2-1 at Avellaneda. Martin Rolle and Julio Furch had the hosts 2-0 up before Harola Reina pulled a goal back.