The African Union (AU) suspended Sudan on Thursday, demanding a "civilian-led transitional authority" to resolve an entrenched and bloody crisis.
Calls for the AU to take action had mounted after Monday's crackdown on protesters who had camped outside army headquarters in Khartoum.
Sudanese authorities admitted dozens were killed when security forces stormed the long-running sit-in.
The Sudan Doctors Committee, one of the protest groups said Wednesday that 40 bodies had been pulled from the Nile, sending the death toll to at least 108.
I said it was not known where they were taken. The committee also said more than 500 have been wounded in the crackdown.
"The AU Peace and Security Council has with immediate effect suspended the participation of the Republic of Sudan in all AU activities until the effective establishment of a Civilian-led Transitional Authority, as the only way to allow Sudan to exit from the current crisis," the AU posted on Twitter.
Patrick Kapuwa, the chairperson of the AU's Peace and Security Council, said the military leadership that took control after the ouster of long-time president Omar al-Bashir in April had failed to hand over power to civilians.
"Council will automatically impose punitive measures on individuals and entities that have obstructed the establishment of civilian-led authority," he said.
Thousands of demonstrators had remained defiant since Bashir's ouster, taking to the streets calling for the generals to cede power to civilians.
The 55-member AU had been strongly supportive of the protesters.
It had urged the military council to ensure a smooth transition of power, warning they risked suspension otherwise.
The organization reiterated this ultimatum in May, giving the military a new 60-day deadline.
But the brutal dispersal of protesters, condemned by the United Nations, US and Britain, among others, put pressure on the AU to beef up its response.
Meanwhile, Sudan's pro-democracy leaders vowed Thursday to press their campaign of civil disobedience until the ruling military council is ousted and killers of protesters are brought to justice.
The Sudanese Professionals Association, an umbrella of union groups that has been behind months of rallies that forced the military to oust Bashir in April, urged people to block main roads and bridges to "paralyze public life" across the country in retaliation for the military's crackdown.
The crackdown began with a violent dispersal of the protest movement's main sit-in camp, outside the military headquarters in the capital, Khartoum, on Monday.
"Our success depends on our full adherence to peaceful protests, no matter how hard the criminal militias seek to drag us into violence," the association said in a Facebook statement on Thursday.
Word about the retrieval of the bodies from the Nile came as Sudan's ruling general called for a resumption of negotiations with the protest leaders, which they promptly rejected. They said the generals cannot be serious about talks while troops keep killing protesters.
The protesters said that instead, they would continue their demonstrations and strikes seeking to pressure the military into handing over power to a civilian authority.
Since Monday's violent dispersal of the protest sit-in outside the military headquarters in Khartoum, violent clashes have erupted in other parts of Sudan.
The protest leaders said there were attacks in 13 cities and towns this week perpetrated by security forces and the paramilitary Rapid Support Forces, which grew out of the Janjaweed militias used by al-Bashir's government to suppress the Darfur insurgency in the 2000s, a campaign that prompted charges of genocide against its perpetrators.
Before Monday's crackdown began, the military and protest leaders had for weeks negotiated the makeup of a transitional council meant to run the country until elections. The protesters demanded civilians dominate the council, which the generals resisted.
After the crackdown, the military suspended the talks and canceled all agreed-on points. It also announced the military would form a government and hold elections within seven to nine months.
But the head of the military council, Gen. Abdel-Fattah Burhan, then on Wednesday abruptly announced the generals were prepared to resume negotiations- an offer the protesters immediately turned down.
In Moscow, a top diplomat said Russia - which has largely stayed on the sidelines of the crisis in Sudan - opposes "any foreign intervention" and believes a compromise is needed.
Mikhail Bogdanov, chief of the foreign ministry's Middle East desk, told local news agencies that Russian diplomats are in touch with all political players in Sudan, including the opposition. Bogdanov visited Khartoum earlier this year.