Worshippers ushered him out of the building and a gunshot - thought to have come from a "blank-firing handgun" - was then heard.
No injuries or damage were caused, Scotland Yard said, and it did not believe the incident was terrorism-related.
Evening prayers were being held at the mosque, off High Road, at the time.
Attack fears
The Met Police said: "Officers, including firearms officers, attended. There were no reported injuries or damage to the building.
"At this early stage, ballistic evidence recovered from the scene suggests that the weapon was a blank-firing handgun."
Officers will remain at the scene overnight, it added.
In a statement shared by a Muslim Council spokesman on Twitter, the mosque's imam Mufti Suhail said the suspect's motives had not been established.
He asked that people "avoid speculating and circulating unconfirmed information".
There are heightened security concerns at places of worship around the world after recent attacks.
A mass shooting at a mosque in Christchurch, New Zealand, in March, left 50 people dead.
In April, churches in Sri Lanka were targeted on Easter Sunday in a terror attack which killed at least 253 people.
A week later, a woman was killed when a gunman opened fire at a synagogue in California.
