The statement, which called the casualties regrettable, added that several people were injured at the protests.
Earlier Friday, Park's presidency ended after a Constitutional Court upheld a December impeachment by South Korean lawmakers.
South Koreans, both supporters and opponents of the former leader, took to the streets by the thousands in emotional, sometimes violent scenes.
Some pro-Park demonstrators, who had been corralled by police in riot gear and strategically placed police buses around 200 meters (650 ft) from the Constitutional Court, rocked the buses in an attempt to overturn them, while others clambered on the roofs of neighboring vehicles.
"We lost our liberty. We lost our Korea," one protestor told Paula Hancocks live on air.
"We cannot understand impeachment for our president," another said. "She is still our president, tomorrow she will be our president."
CNN witnessed some protesters collapsing as a combination of emotion and exhaustion overcame them.
Those who opposed Park's presidency celebrated wildly as the verdict was delivered on live TV. Many endured long, freezing nights protesting her tenure as leader, camping out through long winter nights holding candlelit vigils.
They will likely hold another candlelight vigil, as a last celebration, as night falls.
The unprecedented decision was unanimous, with all eight judges on the court voting to remove Park, the country's first female president, from office. South Koreans immediately took to the streets, with some groups protesting against the decision and others celebrating her removal from power.
The decision was revealed by Justice Lee Jung-mi Friday in a live broadcast that gripped the nation.
"We announce the decision as the unanimous opinion of all judges. We dismiss the defendant President Park," said Lee.