The onlooker was watching the anti-immigration march from the St Denys footbridge over Thomas Lewis Way when he threw the item.
Police were quick to bundle the man to the ground after the incident.
READ MORE: Hundreds line the streets for anti-immigration protest – live
The footbridge was then blocked off by police.
The man was led away from the scene by three police officers, and the force has since confirmed an arrest has been made.
A spokesperson fort Hampshire police said: “Shortly after 2pm, officers quickly responded to a report that a bottle had been thrown from a footbridge in St Deny’s. No injuries were reported.
 “A 45-year-old man from Southampton was arrested on suspicion of a public order offence. He remains in custody while our enquiries continue.”
Hundreds of people are taking part in an anti-immigration and anti-racism protests in the city today.
A large police operation is in force.