A drunken crowd of around 300 gathered blocking roads, throwing missiles and reportedly singing "pro-IRA songs".
The disturbance lasted for over two hours as police attempted to disperse the drunken crowd who were damaging property.
One police officer told the BBC that some people in the crowd had been singing "pro-IRA songs".
It ended at around 4.30am and police remained in the area.
Hundreds are now gathering again in the south Belfast area.
Police are "concerned" that more trouble might break out.
"We're dealing with people who are abusing alcohol and then abusing the community within which they live," Chief Superintendent Chris Noble told the BBC.
"What young people do could have a life-changing effect for them in terms of their education and their employment."
An officer was injured when he was struck on the shoulder by a bottle.
Three males aged 19, 20 and 21 were arrested on suspicion of a number of public order offences.
They have since been charged following the disorder.
The 21-year-old man has been charged with disorderly behaviour, a 19-year-old man has been charged with riotous behaviour while a 20-year-old man has been charged with disorderly behaviour, obstructing police, resisting police and two counts of assault on police.
All three are due to appear at Belfast Magistrates Court on Wednesday April 13.
As is normal procedure, all charges are reviewed by the PPS.
Police have said they will maintain a visible presence today and in the coming days.
Superintendent Darrin Jones said: “Police will continue to have a highly visible presence in the area over the coming days. I want everyone to enjoy the St. Patrick’s Day celebrations but I would strongly encourage people to consider the long term consequences of engaging in drunken or anti-social behaviour.
"Police will deal robustly with any offences to bring people before the courts, and this may lead to career limiting sanctions. Police will be on the streets of Belfast throughout the day to ensure anyone wishing to travel, work or socialise in Belfast can do so safely.”
MORNING AFTER CLEAN-UP
A clean-up operation is currently underway in the area where students are queuing in large numbers at off-licences as they prepare for St Patrick's Day celebrations.
QUEEN'S UNIVERSITY BELFAST CONDEMN BEHAVIOUR
A spokeswoman for Queen's University Belfast said that they will have a team on the ground today and that any student found to have brought the university into disrepute will face rigours of "strict off-campus disciplinary code".
It said in a statement: "Queen’s University and the Students’ Union condemn the anti-social behaviour that took place in the Holyland area of Belfast last night. Staff from the University and the Students' Union are on the ground today in the Holyland area, as they will be tonight.
"While the vast majority of Queen’s students will celebrate St Patrick’s Day in an enjoyable and peaceful manner, Queen’s will fully investigate any complaints or reports of anti-social behaviour.
"A strict off-campus disciplinary code is in place and if any Queen’s student is found to have brought the University into disrepute, they will be subject to the full rigours of this code. The University has been working since January of this year with the PSNI, Belfast City Council, Ulster University, Belfast Met and other key stakeholders, and supports robust enforcement of legislation in relation to anti-social behaviour. The University will continue to liaise closely with the authorities in identifying any Queen’s students who may have been involved..
"Over the last number of years the University has invested significant resources to help improve community relations and will continue to work with its partners to this end.”
ULSTER UNIVERSITY HAD 'TEAM ON GROUND'
In a statement to the BBC Nolan Show Ulster University said they had a team on the ground at the time of the disorder and will have a presence in the area throughout the day.
A spokesman said: "Although the activity in the Holyland area is a combination of university and college students, non residents and post primary students all five HEI's have been working proactively together in advance of St Patrick's day to ensure their respective students are fully aware of their responsibilities and risks of engaging in anti-social behaviour.
"We have built strong partnerships with Belfast City Council, landlords, residents and police who are supportive of our ongoing work in the area.
"We are and have been working closely with them throughout the year.
"A new joint community affairs officer funded by Ulster University and Queen's University Belfast enaged with students on a daily basis
"We can confirm that the Ulster University had a team on the ground last night and will have teams in the area throughout the day."
'DISPERSE STUDENTS FROM HOLYLAND ACCOMMODATION'
South Belfast MLA Máirtín Ó Muilleoir called the disruption "unacceptable" and called for Stormont's Department of Social Development to disperse the students from the Holyland.
He said: "While people are entitled to celebrate holidays like St Patricks Day there is absolutely no justification whatsoever for the behaviour which Holyland residents had to endure last night.
"The core issue within the Holyland has always been the concentration of students into a small area. Sinn Féin had taken a position some time ago that purpose built student accommodation would help resolve this. Thankfully we have seen a number of these developments across the city been approved by planners. I believe this will help to relieve the Holyland issue.
He added: "I would go further and call on the DSD to plan for a dispersal of students from the Holyland allowing the properties there to be transformed back into family homes.
"For today however, I would urge students and others to not let the behaviour we witnessed last night be repeated and to enjoy St Patricks Day in a responsible way with due regard to the Holyland community"
'ATTACKING POLICE HAS NOTHING TO DO WITH ST PATRICK'
DUP MLA for south Belfast Emma Little Pengelly slammed the disturbance as "disgraceful and provocative".
She said: "Crowds singing pro-IRA songs while attacking police with bottles has nothing to do with St. Patrick. It is sectarian, totally unacceptable and it needs to stop.
"I have been working closely with Queen’s University, Ulster University and others in the lead up to this year’s St Patrick’s Day working hard in the background to try and prevent anti-social or drunken behaviour on the streets.
"It is disgrace that once again, despite these efforts, we have a situation today where a police officer has been injured and three people arrested. This is absolutely shameful.
"I will continue to liaise with the PSNI and the University contacts throughout today in attempts to prevent more disorder.”