The youngster had gone to Glasgow Green with relatives to watch as the parade arrived on Saturday afternoon.
Fighting then broke out among a handful of spectators, during which the young girl was struck in the face by a bottle that had been thrown.
An eyewitness said: "There were hundreds of people in the park and there was a group of about 25 who started shouting at each other.
"They had been marching with the parade and were wearing scarves and waving their flags.
"This big fight erupted and both sides were kicking and punching one another. Then I saw a young girl screaming - it was horrendous."
Another witness said: "I saw this girl out the corner of my eye coming across the grass screaming. It looked like she was cut across her forehead, there was a lot of blood."
The girl was treated at Yorkhill hospital and has since been released.
Police made 18 arrests in the wake of the violent scenes and say they will be continuing their investigations.
A spokeswoman said: "We can confirm Police Scotland is investigating a serious assault on a 12-year-old girl on Saturday, July 5.
"A number of people nearby became involved in a fight which resulted in the girl being struck with a bottle or similar object.
"An investigation is ongoing to establish the full circumstances and trace those responsible."
Officers have asked anyone with information to call Police Scotland's London Road station or the non-emergency helpline 101.
The clashes have raised concerns over the nature of the Orange Order marches and their propensity for attracting violence.
Yesterday, those angered by the scenes started an online petition addressed to Glasgow City Council in an attempt to end further marches in the city. Within hours, thousands had signed up.
Edward Hyde, County Grandmaster of Glasgow and Grand Secretary of the Orange Lodge of Scotland, blamed Saturday's unrest on an unwelcome minority of supporters.
He said: "These people are a total embarrassment to us. We are doing our best to rid ourselves of that element and we will get there."
The Order officially aligned itself with the pro-union parties in the Scottish referendum, although the Better Together campaign has denied any ties with the group.
The Orange Order is currently proposing to hold a rally in Edinburgh in the run-up to the referendum. Council officials in capital would not comment on whether the scenes in Glasgow would affect its decision, due to made later this month.
A spokesman said: "We have received an application for Orange Order to hold a march on September 13.
"The council will now consider the proposal when licensing sub-committee meets on July 23."