Former title winners Gremio drew 1-1 away to the Chilean champions to advance from Group Eight with fellow Brazilian side Fluminense, 1-0 winners at home to Caracas FC.
Brazilian champions Flu finished top of the group with 11 points, three more than Gremio and Huachipato, who were separated by goal difference.
TV replays showed former Real Madrid and Brazil coach Luxemburgo laughing at his opposite number Jorge Pellicier as he ran towards the tunnel after the final whistle, then falling over as Huachipato players appeared to attack him.
This was followed by mayhem on the edge of the pitch and at the entrance to the tunnel as players, coaching staff and invading Huachipato fans became embroiled in a brawl with Chilean police frantically trying to put a stop to it.
"I didn't say anything or provoke (anyone). I saw they were looking to fight so I ran off," Luxemburgo said.
Pellicier, however, disputed that version of events when quoted by the Chilean daily El Mercurio's website: "He tried to make fun of us... That's unsporting conduct. He said we should go on holiday, making a gesture with his hand."
It was a sorry end to a good match in which Gremio, champions in 1983 and 1995, went ahead when Ze Roberto opened the scoring with an overhead kick.
Huachipato defender Miguel Aceval equalised with a curling left footed free kick past Gremio's former AC Milan and Brazil goalkeeper Dida one minute from time in a dramatic finish.
Fluminense, who scored through former Brazil striker Rafael Sobis, qualified for a last-16 clash with Emelec of Ecuador while Gremio will meet Colombia's Independiente Santa Fe.
With six Brazilian sides in the last 16, holders Corinthians face six times South American champions Boca Juniors of Argentina in the pick of first knockout round ties.
In a tight Group Eight, modest Argentine side Tigre upset Libertad of Paraguay 5-3 in Asuncion to snatch the second qualifying berth behind former champions Palmeiras of Brazil.
Palmeiras, who lost 1-0 to Sporting Cristal of Peru in Lima, and Tigre both finished with nine points, separated by a goal difference of one. Libertad and Cristal ended up with eight points.
"The truth is that last (Libertad) goal was incredible, we were 30 seconds from finishing top (of the group)," said Matias Perez Garcia, who scored twice for Tigre.
"Never mind, we got what we came for. Tigre are alive after we'd been left for dead. We showed character," added the striker, whose side had gone into the match in third place.
Tigre earned a clash with another Paraguayan side, three times champions Olimpia, while Palmeiras, relegated to Brazil's second division, meet Mexico's Tijuana.
- Sports & Recreation