Jailed cleric Abu Hamza al-Masri is known to have given sermons at the mosque.
Around 20 demonstrators calling themselves members of the United British Alliance waved UK flags and shouted anti-Muslim insults from behind a barricade set up by police.
A couple of the men managed to jump the barrier and interrupt prayers being held in the street in front of the mosque in Finsbury Park, in the north of the capital.
Police broke up the skirmish immediately, and prayers resumed while protesters sang traditional British national songs.
Abu Hamza was arrested in London last Thursday and is in custody ahead of an extradition hearing concerning 11 terrorism-related charges brought against him by the US.
The mosque was closed 18 months ago but Abu Hamza continued to preach in the street each Friday.
Police chief Barry Norman said an extra 60 officers had been deployed around the prayer site and security fences thrown up to protect Friday prayers for the 50 or so Finsbury Park worshippers.
Several of the Muslims there, some wearing masks, announced a protest later on Friday in front of the US embassy in London, and distributed leaflets denouncing the “persecution” of Muslims by US President George Bush and British Prime Minister Tony Blair.