The MLS disciplinary committee hit Schallibaum with his third suspension of the season after the Swiss coach stepped onto the field during the Impact's home loss to Colorado on Saturday.
The Impact say they tried to appeal the ban as Schallibaum was not ejected from the game or sanctioned by the referee for the incident.
Impact assistant coach Philippe Eullaffroy was also suspended for one game for throwing the ball in the direction of Rapids midfielder Tony Cascio.
Assistant coach Mauro Biello will replace Schallibaum for tonight's game.
MLS also announced that Toronto FC and head coach Ryan Nelsen were fined an undisclosed amount for the team's violation of the league's mass confrontation policy during a 78th-minute altercation in a 1-0 home loss against Real Salt Lake on Saturday.
The team had previously received a warning from the league about mass confrontation earlier this season.
MLS defines mass confrontation as the concerted efforts of three or more players toward an official or an opposing player. The policy was introduced prior to the 2013 MLS season.