Worshippers offered prayers for Drummer Rigby and his family and expressed solidarity against extremism.
National president of the Ahmadiyya Muslim Association UK Rafiq Hayat said: "We stand united with the rest of the country in sharing the deep sorrow and pain following the horrific senseless attack on Wednesday.
"Our thoughts and prayers are with the family of Drummer Lee Rigby. We hope that the perpetrators of this crime, that is based on a twisted and warped ideology, are brought to justice.
"Islam is a religion of compassion and peace; a religion which considers the killing of an individual akin to killing the whole of humankind. Such acts of violence, therefore, have absolutely no place in Islam and can never be justified."
Similar condemnation was echoed in mosques throughout the UK.
Police have since deployed officers to guard Morden mosque after threats appeared on social media sites, Facebook and Twitter, calling for it to be burnt to the ground. The mosque was targeted on a Facebook page named 'True British Patriots'.
Users on the page referred to Muslims as “f****** muzzies” and called for mosques in Morden, Watford and Braintree in Essex to be burned to the ground.
Drummer Rigby, from Langley, in Greater Manchester, was from 2nd Battalion, The Royal Regiment of Fusiliers, had served in Afghanistan and was attached to the Regimental Recruiting Team when he was hacked to death on Wednesday afternoon.
Two suspects were shot and arrested at the scene and remain in police custody.
Meanwhile nearly 100 senior British imams have signed a letter condemning the Woolwich attack.
The letter read: "We share the absolute horror felt by the rest of British society at the sick and barbaric crime that was committed in the name of our religion. We condemn this heinous atrocity in the strongest possible terms.
"It is a senseless act of pure depravity worthy of nothing but contempt. There can be no justification for murder."
The document was signed by 94 imams, including Shaykh Ibrahim Mogra, assistant secretary general of the Muslim Council of Britain.
It said that imams and Muslim organisations had spoken out "over the evils of terrorism" for many years, but recent events showed they cannot afford to be complacent.
The imams also criticised some incidents which occurred in the aftermath of the killing.
"Already we have seen extremists seeking to capitalise upon Wednesday's terrible act. There have been several attacks reported against mosques and Muslim citizens," they wrote.
"The hate-fuelled individuals behind such attacks wish to polarise and tear apart our great country for their own sick ends. They should be isolated and subject to the full force of the law."
The letter went on: "We the British people are not so easily fooled; nor are we so easily divided. The overwhelming majority of the Muslim community stands united with the rest of society in condemning this awful tragedy."
Tensions remain high across the UK following the murder. Police have vowed to take a zero tolerance approach to religious or racially-aggravated attacks.