Jesus tested positive for COVID-19 on Monday, though it was weak or inconclusive and being checked.
The 65-year-old Portuguese was cleared of the virus on Wednesday amid the pandemic, which has claimed almost 9,000 lives globally.
"Flamengo inform the new exam carried out by coach Jorge Jesus confirmed a negative result for COVID-19," the club said via Twitter.
O Clube de Regatas do Flamengo informa que o novo exame realizado pelo técnico Jorge Jesus atestou resultado negativo para o Covid-19. O clube agradece pelo suporte de toda Nação Rubro-negra ao Mister nos últimos dias. #CRF— Flamengo (de 🏠) (@Flamengo) March 18, 2020
"The club are grateful for the support of the entire Red-Black Nation to the Mister in the last days."
Jesus has enjoyed great success at the helm of Flamengo since arriving in 2019, leading the club to Campeonato Brasileiro, Copa Libertadores and Recopa Sudamericana glory.
After winning a second Libertadores title and first since 1981 in November, Flamengo were crowned Brazilian champions for the seventh time last year, having not claimed the Campeonato Brasileiro since 2009.
Flamengo then added the Recopa – which pits the Libertadores and Copa Sudamericana champions against each other – to their collection in February.