Amess, 69, was knifed at a church on Friday in Leigh-on-Sea, east of London. At the scene, police arrested the 25-year-old son of an ex-media adviser to a former Somali prime minister. He remains in custody.
They are treating the attack, which Johnson described as a "contemptible act of violence," as potential terrorism.
Speaking to the congregation, the Archbishop of Canterbury said there was " a unanimous conviction" that Amess was "of the best".
The service was held at St Margaret's Church in Westminster and came after two hours of tributes to Amess from colleagues in parliament.
The murder of Amess has prompted questions about politicians' safety and what should be done to address the growing problem of online abuse.
Detectives are quizzing suspect Ali Harbi Ali, a British national, under counter-terrorism laws, looking at a possible link to Islamist extremism. Officers are also searching properties in and around London.
Ali had been referred to a anti-radicalisation programme known as Prevent, the BBC said. But he was not of formal interest to the domestic security agency MI5.
Amess was also chairman of the cross-party committee which promoted good ties between Britain and Qatar, and the Times newspaper said detectives were looking at this link. Amess had visited Qatar last week.
Police have warned about the danger the COVID-19 pandemic posed in terms of radicalisation as vulnerable people spent more time online, potentially exposed to extremist material.