Round-up: Crowd violence mars Caracas win
Nacional's Fabio Escobar was sent off for spitting at an opponent as his team lost 3-1 to Paraguayan champions Libertad, who stayed in the hunt for a fifth consecutive title.
Caracas FC came from a goal behind to win 3-1 at Zamora FC and win the second stage of the 2008/09 championship.
Caracas leapfrogged defending champions Deportivo Tachira, who were held 3-3 at home by Estudiantes de Merida, and will meet Deportivo Italia, winners of the first stage, in the two-leg, end-of-season final.
The second half of the match in Barinas was delayed for 10 minutes as rival fans in the 8,700 crowd clashed on the terraces.
Local media said Caracas fans hurled objects, including plastic seats, at the home contingent and police used tear gas to stop the trouble.
Orlando Cordero put Zamora ahead two minutes after the game eventually re-started but Rafael Castellin scored twice in three minutes to give Caracas the lead.
Defender Jose Manuel Rey completed the scoring with a trademark free kick late in the game.
Caracas completed the 17-match programme with 37 points, one ahead of their arch-rivals Deportivo Tachira.
Daniel Arismendi gave Tachira a 31st-minute lead but William Diaz levelled three minutes later and Duvier Riascos put the visitors ahead just before the hour.
Although Gerson Chacon made it 2-2 in the 77th minute, Angelo Pena put Estudiantes back ahead eight minutes later and Marlon Fernandez's 90th-minute goal for Tachira was too late.
Libertad, winners of the last four championships, closed the gap on leaders Cerro Porteno with a 3-1 win over Nacional.
Juan Samudio converted a third-minute penalty for Libertad, Manuel Maciel added a second before halftime and Miguel Samudio made it 3-0 early in the second half.
Nacional had Escobar sent off for spitting at Libertad's debutant teenager Victor Ayala as the two argued at the end of the first half.
Libertad had Omar Pouso sent off for the second match running in the second half.
Libertad moved within four points of Cerro Porteno, who were held to a goalless draw by 2 de Mayo, and have a game in hand.
Defending champions America missed out on the playoff stages of the Apertura championship, their final hopes evaporating in a 3-1 defeat at Millonarios.
They were one of several big clubs who failed to qualify alongside Millonarios themselves, Santa Fe, Independiente Medellin and Atletico Nacional.
Deportivo Cali qualified by drawing 2-2 at home to Santa Fe in a match played behind closed doors following a pitch invasion during a cup game against America earlier this month.