Victoria Police interviewed the man over the incident and said he will be charged with assault by kicking.
The charges for the man who has not yet been named, came after police appealed to the public for help with tracking him down.
Investigators allege he kicked 17-year-old Mr Connolly several times while he was on the floor being held down, News.com.au reports.
Mr Connolly egged Queensland senator Fraser Anning after the politician made inflammatory remarks about Muslim migration following the Christchurch shootings in New Zealand in which a white supremacist massacred 50 Muslims in two mosques.
In the moments after the egging, which was caught on camera, Mr Anning turned and struck the teenager twice in the face before Mr Connolly was wrestled to the ground.
Last week Mr Anning's colleagues in the Australian Parliament passed a censure motion against him saying his statements blaming the victims of the massacre were ugly and dangerous.
On Tuesday Victoria police said neither Mr Connolly nor Mr Anning were to be charged after the incident.
After reviewing the footage and interviewing both of them, they only issued an official caution to Mr Connolly.
Mr Connolly’s lawyer Peter Gordon released a statement saying the decision not to charge the 17-year-old was a “relief” and the last few weeks had been a stressful time for him and his family.
“Will is taking very seriously the formal caution he was given by police about his actions,” the statement said.
“Will and his family at no stage sought to have any action taken against people who reacted against him following the incident,” he said.
The man allegedly kicked 17-year-old Will Connolly while the teenager was being held down by several men (EPA)
Mr Gordon also said money totalling more than A$100,000 (£55,000) donated through a crowd funding page originally set up to pay any legal costs Mr Connolly incurred and for “more eggs”, would be donated to help victims and families of the Christchurch tragedy, as per Mr Connolly’s wishes.
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