Rooney, who will depart America to head to Derby County in January, launched a furious outburst at the fourth official after being substituted in the 72nd minute.
He was seen screaming "Every f****** game" at the official before he eventually headed to the bench, appearing to be angry at the level of officiating in the American top flight.
He then took aim at travel arrangements in the league immediately after the game, complaining about their 12-hour trip back from Canada ahead of a midweek clash with New York Red Bulls.
Rooney tweeted: “Gutted about result last night. We deserved more. Looking forward to a 12 hour travel day which could be done in 6 but hey this is mls. We will get ready for red bulls Wednesday. #Charterflights #mls."
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