A potential winning goal in the 90th minute by Toronto's Gilberto was called off by Canadian referee David Gantar who said later the Brazilian forward was guilty of a pushing foul. The game ended at 1-1.
"That referee did not get it right in that game, and we shouldn't be ashamed of saying that," Garber said Thursday. "I feel for Toronto FC."
The commissioner said he had expressed his concerns to Peter Walton, general manager of the Professional Referee Organization.
Garber also said the league is reviewing Toronto midfielder Michael Bradley's post-game criticism of Gantar.
"Michael is the leader of that club," Foxsports.com quoted Garber as saying after unveiling the new MLS logo in New York. "He's been an asset to the league. I have tremendous respect for him. We'll take a close look at it and see if there is any discipline required. But I understand and sympathize with his frustration."