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Late in Sunday's game at Epping Stadium, play had to be stopped for several minutes as the referee, City captain Emma Checker and Victory skipper Angela Beard attempted to calm the crowd down.
It took the gloss off City's thrilling 3-2 win, which was a remarkable turnaround from their 6-0 loss to the same team a week earlier.
City coach Rado Vidosic condemned the behaviour as "not acceptable" and lauded the referee's swift action.
"Come here, support your team, that's brilliant ... but to throw things at a goalkeeper, a female goalkeeper - and she's a Matilda - I don't think that's the right way of dealing with the situation," he said.