The Galaxy won the Western Conference semi-final, first leg tie 1-0 and at the final whistle Galaxy's Mexican defender Rafa Marquez lobbed the ball at Donovan, hitting the winger on the leg.
The incident prompted Galaxy's Adam Cristman to confront Marquez, who lunged with his head at the American and in the fracas that followed Galaxy's Brazilian midfielder Juninho appeared to elbow a Red Bulls' player.
After the game MLS said that both Marquez and Juninho had been given red cards and would miss the return leg at Galaxy's Home Depot Center on Thursday.
But Donovan ensured the dispute continued, in verbal form at least, with his post-game comments to reporters.
"There were a few plays where they took some cheap shots at us," he said, "In all my years in this league, I've not played against a cheaper team, and they've been doing it all year," he added.
"We saw it a few weeks ago with [Thierry] Henry kneeing someone in the back. We've seen that stuff all year. You just deal with it, and at the end of it, the cream rose to the top, and the better team won," he said.
Not all of Donovan's team-mates agreed.
"They are a good soccer team," said goalscorer Mike Magee, a former Red Bulls player. "We lost our heads too, so we can't point the finger at them."
The incident is not the first indication of bad blood between Donovan and the New York team.
After a game between the teams in May, his behaviour towards Henry was criticised by Red Bulls' English forward Luke Rodgers.
Donovan responded on his Twitter page, saying: "I am confused; who is Luke Rogers?"
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