Friday was declared a national holiday for the funeral, and citizens, including school children in uniform, lined the roads waiting for the funeral convoy to pass.
Inside the stadium the arrival of Nkurunziza’s remains led to screams, tears and moans from the crowd, who were asked to stand in silence and bow.
The majority were not wearing masks or respecting social distancing guidelines.
Burundi has taken few measures to combat the spread of the coronavirus, with Nkurunziza claiming God had spared the country from its ravages.
During his swearing-in ceremony, Ndayishimiye admitted the dangers posed by the virus, and urged Burundians to take care and go to a doctor if they felt ill.
Since announcing its first case in mid-March, Burundi has only officially recorded 144 cases and one death.
A medical source told AFP that Nkurunziza had suffered “respiratory distress” before dying.
One diplomat attending the funeral told AFP he had arrived with a mask but removed it after feeling “ridiculous” as no one else was wearing one.
The coffin carrying the late president arrived at a stadium in the city, covered in the green, red and white national flag and borne atop a military jeep, as soldiers marched in step alongside it.
The funeral convoy was welcomed by a military band after a 60km journey from the city of Karusi where Nkurunziza, 55, died on June 8 of what the government said was heart failure.
However speculation is rife he may have caught the coronavirus, as his wife had been flown to Nairobi for treatment for the virus just two weeks prior.
The ceremonies began early in the morning with a “homage by his wife, Denise Bucumi Nkurunziza, his children and those close to him” in an intimate gathering at the hospital where he passed away, a government source told AFP.
Nkurunziza died shortly after an election won by his handpicked successor Evariste Ndayishimiye, who was sworn in last week and who presided over the funeral.
“Nowhere in Africa, or the world, has a leader been as close to God as president Nkurunziza was,” Ndayishimiye said in a tear-filled speech, adding he was also “the closest to the people”.
“We have lost a father, a friend, a saviour and a head of state,” he said.
Nkurunziza’s wife Denise, who has recovered from the virus, said that God had given her the strength to accept what had happened.
“In the Bible it is written that we must accept God in everything. There was nothing else to do and I did it,” she said..
Nkurunziza, a devout evangelical who believed he was chosen by God to lead Burundi, leaves behind a deeply isolated country in political and economic turmoil.
His 2015 run for a third term in office sparked protests and a failed coup, with violence leaving at least 1 200 dead while some 400 000 fled the country.
A climate of fear marked by a crackdown on the opposition and media settled over Burundi, while a personality cult grew around Nkurunziza which saw the ruling party name him a “visionary” and “supreme guide for patriotism.”
UN human rights investigators have said the period since 2015 has been marked by likely crimes against humanity committed by state forces, citing extrajudicial executions, arbitrary arrests, disappearances, torture and sexual violence.