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.
"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.
The Brazilian Serie A champions announced on Monday that Jesus, 65, has tested positive for COVID-19, although it was weak or inconclusive and being checked.
In a message posted on Instagram, Jesus said he was asymptomatic despite the positive test.
"Hello. Good afternoon in Brazil, good night in Portugal. True, my test was positive," he said.
"It is also true that I feel normal, I am feeling exactly as I felt a month ago, a year ago, two, three, four... I am normal. I don't feel any symptoms.
"But I had a positive test. I'll be in reclusion. I want to thank the affection of my friends and the fans of Flamengo for sharing this situation with me.
"I think that in a few days everything will be back to normal, God willing. A big kiss to everyone. I am very confident."
The Brazilian Football Confederation (CBF) announced the suspension of all national football competitions for an indefinite period on Sunday.
Jesus, 65, took the helm of Flamengo last year and led the club to three trophies in 2019, winning the Copa Libertadores, Brazilian Serie A and Campeonato Carioca.
The former Benfica boss confirmed he had agreed to a new deal on Tuesday, with reports suggesting he will earn around €4million.
"My representatives reached an agreement today with Flamengo's board of directors to renew my contract for another year," Jesus wrote on Instagram.
"My friendly relations with the entire squad, club structure and Flamengo's fans were decisive to touch my heart and spoke louder in my decision.
"Thank you all for your kindness and support."
Jesus has led Flamengo to 41 wins from 55 games since taking charge in June last year.
The Copa Libertadores success last year was Flamengo's first since 1981.
Former Arsenal and Real Madrid playmaker Ozil has a contract that runs to the end of the 2023-24 season but was banished from first-team duties in March.
Reports claimed that decision came after a dispute with interim head coach Ismail Kartal, and Ozil may have hoped the appointment of Jesus would change his circumstances.
Yet a return to action for Fenerbahce seems as far away as ever after former Benfica and Sporting CP boss Jesus declared Ozil does not figure in his plans.
"What you have achieved in the past in football is very important. Mesut Ozil has a very important past, but the club has made a decision about him, and he will continue in the same way," Jesus said at a news conference held to announce his arrival.
Jesus added, according to Turkish news outlet Hurriyet: "The important thing here is not Jorge Jesus, Mesut Ozil or any other person. Fenerbahce is important."
Fenerbahce signed Ozil from Arsenal in January 2021 after he fell out of favour with the Premier League club, with the deal considered a major coup at the time.
After a second-placed finish in the 2021-22 Super Lig, Fenerbahce are hoping to bring in four or five new players, said club president Ali Koc, who added: "We will focus on players who will be decisive offensively."
They might have hopes of offloading Ozil, but the 33-year-old former Germany international said this week he has no intention of leaving the Istanbul giants.
Ozil wrote on Instagram: "I repeat with emphasis; I will not end my career in a team other than Fenerbahce.
"This decision is very clear and final. As per the requirements of professional life, if our management takes a decision about me, I will only respect this attitude. I will work hard and always keep myself ready."
