Argentine striker Luciano Figueroa equalized with a header in the 83rd minute and Fernando Gaibor scored the winner from the penalty spot in the 90th in a dramatic match at a packed George Capwell stadium.
A home loss would have eliminated Emelec from Latin America's most important club competition. Ronaldinho's Flamengo, meanwhile, dropped to last place and will need to beat Argentina's Lanus at home in the last round and hope Olimpia draws Emelec in Paraguay. Any other result will eliminate the team coached by Vanderlei Luxemburgo.
The result in Ecuador guaranteed Lanus a spot in the second round from Group 2. Lanus has 10 points, three more than Olimpia. Emelec has six points and Flamengo five. Only the top two teams in each of the eight groups advance to the second round.
Flamengo opened the scoring via right back Leo Moura in the eighth minute and Figueroa equalized with a header in the 34th. Striker Deivid put Flamengo ahead again in the 43rd but the Brazilian club was not able to hold on. Flamengo had already allowed two late goals in a 3-3 draw with Olimpia in its previous match.
Also Wednesday, defending champion Santos moved into good position to advance from the group stage with a 1-1 draw against fellow Brazilian club Internacional.
Santos reached 10 points to stay atop Group 1, two points ahead of Internacional. The Strongest of Bolivia is third with seven points, but it can move up the standings if it beats last-place Juan Aurich in Peru on Thursday. Juan Aurich has lost all of its four matches.
Defender Nei scored for Internacional with a well-struck free kick in the ninth minute, and Alan Kardec equalized for Santos with a diving header from near the penalty spot in the 66th, just two minutes after entering the match.
A victory would have been enough for Santos to secure a spot in the second round. In two weeks, Internacional will play at Juan Aurich while Santos will host The Strongest.
Brazil striker Neymar was a constant threat for Santos but failed to capitalize on his scoring chances.
Internacional defender Rodrigo Moledo was sent off with a second yellow card after a foul on Neymar in the 89th.
The match in front of nearly 40,000 fans at the Beira-Rio stadium pitted the last two Copa Libertadores champions against each other. Internacional won the competition in 2006 and 2010. Santos' title last year was its third overall, and first since the Pele era.
In Argentina, Universidad de Chile beat host Godoy Cruz 1-0 with a goal by striker Henriquez Iturra three minutes into first-half injury time, moving to first place in Group 8 after five matches.
Universidad de Chile has 10 points, two more than Colombia's Nacional de Medellin and three more than Godoy Cruz, which needs Nacional de Medellin to lose its match against last-place Penarol next week to retain any chance of advancing to the second round.
In Colombia, Junior Barranquilla defeated Universidad Catolica of Chile 3-0. Ivan Velez, Luis Paez and Vladimir Hernandez scored for Junior Barranquilla, which is still last in Group 3 with four points.
Union Espanola and Bolivar have seven points each, while Universidad Catolica has six.