Mexico's America qualified as Group Three winners with Fluminense pipping Nacional, held 0-0 by the Mexicans in Montevideo, into second place with equal goal difference but having scored more. Had Fred not converted the penalty, Nacional would have qualified on a better goals differential.
Paraguay's Cerro Porteno, with a brilliant performance from midfielder Jonathan Fabbro, came from two goals down to beat Colo Colo 3-2 in Santiago and win Group Five ahead of Santos, second after a 3-1 home win over Venezuela's Deportivo Tachira.
On a night of thrilling football, the ugly side of South America's premier club competition emerged at the Diego Armando Maradona stadium in Buenos Aires in a free-for-all between the Argentinos and Fluminense players after the final whistle.
Argentinos goalkeeper Nicolas Navarro, upset by the penalty decision, was at the heart of the punches thrown between home players and Brazilians exultant at their last-gasp qualification having started the night bottom of the group.
"Nothing justifies the violence," Argentinos Juniors coach Pedro Troglio told Fox Sports.
At the Centenario in Montevideo, Nacional thought they were through by a difference of one goal only to learn of Fred's late goal in Buenos Aires that eliminated them. Flu finished with a goals tally of 9-9 to Nacional's 3-3.
Navarro had dashed out of his goal to clear with his foot from defender Edinho, who went down with the referee pointing to the spot. It was unclear from television replays whether Navarro reached the ball first as he appeared to claim.
Left-back Julio Cesar put Fluminense ahead at the end of a fine attacking move midway through a first half dominated by the Brazilian champions.
Paraguayan striker Santiago Salcedo equalised with a penalty but former Brazil striker Fred restored Flu's lead with his first goal, a bullet of a free kick from 33 metres shortly before half-time.
Midfielder Gustavo Oberman hit another equaliser with a shot that took a deflection early in the second half only for striker Rafael Moura to put the Brazilian side ahead again from the rebound after Navarro parried a shot.
FANTASTIC FABBRO
Fabbro scored twice in a thriller at the Monumental in Santiago in which midfielder Cristobal Jorquera and Chile striker Esteban Paredes gave Colo Colo a two-goal start inside 20 minutes.
Man-of-the-match Fabbro pulled a goal back just before half-time with a looping right-footed shot from left into the top far corner then had a hand in Porteno's equaliser four minutes into the second half when he laid the ball off to the right for right back Ivan Piris to blast a low shot into the net.
Fabbro scored the winner with a brilliant, curling free-kick into the top corner in the 88th minute, ushering in a nail-biting five-minute period of added time.
Brazil teenager Neymar, back from suspension, set twice champions Santos on their way to a comfortable win with an early goal at the Pacaembu in Sao Paulo.
