The defendants' lawyers have said they will appeal the decision, while two others standing trial were acquitted.
The death penalty is often handed down in the Democratic Republic of Congo, but it has not been applied for 20 years and is systematically commuted to life imprisonment.
During closing arguments on Friday, a senior public prosecutor had not requested capital punishment but life imprisonment for the main defendant, Colonel Mike Mikombe.
But the court handed Mikombe the death sentence with a charge of "murders", although charges of crimes against humanity were dropped.
The prosecutor also asked for sentences ranging between 10 and 20 years for the five other defendants.
The six soldiers had been on trial since September 5 over the deadly crackdown against a religious sect that called for demonstrations against the United Nations' presence in the region.
The crackdown saw 57 people killed, according to the latest official toll, and has led to renewed tensions in the North Kivu capital of Goma, an area plagued by violence by armed groups.
More than 140 civilians including around 30 minors were also arrested during the August 30 army operation.
- Questions -
In the aftermath, the government quickly announced the arrest of several soldiers and promised justice would be served.
But the trial did not answer all the questions about the circumstances of the killings.
Interior Minister Peter Kazadi has indicated that the elite Republican Guard intervened after the lynching of a police officer by members of the religious sect.
Witnesses -- including two army colonels but also sect members and local residents -- however say the operation began before the police officer died.
The same witnesses have also said that before the killings, negotiations between the army and the sect were progressing well, but the military then suddenly opened fire on the unarmed sect members.
The question remained whether Mikombe gave the order to shoot, and whether he was following orders or acting on his own.
He suggested in court that he had been misled by an operational order identifying the sect members as proxies of M23 rebels and the Rwandan army.
The M23 has captured swathes of territory in North Kivu province since 2021 -- one of several militias holding sway over much of the region despite the presence of peacekeepers.
Independent UN experts, the Kinshasa government and several Western nations including the United States and France accuse Rwanda of actively backing the Tutsi-led M23 -- claims that Rwanda denies.
Mikombe also called on the court to probe the military governor of North Kivu, General Constant Ndima, who was recalled to the capital Kinshasa for "consultations".
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