The former Real Madrid and Brazil coach, alleged to have sparked the brawl, was also fined $25,000 by CONMEBOL, which posted the sanctions on its website.
The heaviest punishment went to Luxemburgo's right hand man Emerson, who was banned for eight matches and fined $20,000.
Luxemburgo appeared to make fun of his Chilean opponents after the final whistle of the decisive Group Eight match at the CAP stadium in the southern Chilean city of Talcahuano which ended 1-1 with Gremio qualifying for the last 16.
TV replays showed Luxemburgo laughing at Huachipato coach Jorge Pellicier as he ran towards the tunnel, then falling over as Huachipato players appeared to attack him.
There was 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.
"As I see it, this (sanction) was totally unjustified. It was a superficial analysis. The provocation came from (Huachipato)," Luxemburgo told a news conference in Porto Alegre, where Gremio are based.
"But if the CONMEBOL saw it that way, all we can do is regret it," added Luxemburgo, as reported by Brazil's Globo network.
"I only escaped the confusion trying to get to the dressing room and laughing at what was happening. If I got six matches for that, it's absurd."
Luxemburgo will not be in charge when former champions Gremio, who finished second to fellow Brazilian side Fluminense in the group, meet Colombia's Independiente Santa Fe in the first leg of their last-16 tie at home on Wednesday.
There were bans and fines issued by the Asuncion-based CONMEBOL for other members of the coaching staff and players of both sides.
Gremio also had central defender Douglas suspended for five matches and fined $10,000.
Pellicier was suspended for one match and fined $1,000 and his team's physical trainer Marcelo Rosemblat one match and $2,000.
Three Huachipato players were handed bigger punishments: a ban of five matches and a $10,000 fine for defender Juan Espinoza, three matches and $5,000 each for midfielders Francisco Arrue and Nicolas Nunez.