Bouts of sporadic trouble flared in the Donegall Road, Sandy Row area from 8pm to 10pm.
Police said protestors blocked the Donegall Road with burning bins and carried out "sustained attacks" on the PSNI with bricks and bottles. One officer suffered minor injuries.
Police arrested an 18-year-old man who has since been released.
Ruth Patterson, of the DUP, said the disturbances started after a group of flag protestors were "taunted" by people celebrating St Patrick's Day.
The local councillor said: "A group of people intended to have a flag protest at one of the bars in Shaftesbury Square and on their way round police stopped them and pushed them back into the Donegall Road when at which point a crowd of people who had been celebrating St Patrick's Day shouted and chanted. That is when trouble ensued.
"The police are there to do a job and we understand that but there seems to be a one-sided agenda at the moment with the PSNI and that is most certainly to come down very heavily on flag protestors while others get away with everything."
Alliance South Belfast MLA Anna Lo said the trouble erupted after protestors "attempted to walk to a bar but were pushed back by police".
"Everybody must unequivocally condemn this trouble. The blame for these disturbances lies solely with the protestors," she said.
"The St Patrick's day celebrations were a great success, so I am disappointed that a tiny minority were intent on trying to ruin the day."
Calm was restored to the area by around 10pm.
Officers from the PSNI's Operation Dulcet inquiry team - who are investigating offences linked to the Union flag protests in Northern Ireland - said they have been "clear from the outset that there will be consequences for individuals who engage in illegal activity."
A statement continued: "The PSNI have and will continue to make people amenable to the courts and will be carrying out further enquiries to identify those involved in the disorder."